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Thanks everyone for your time and attention.
I try to explain again my process
We filmed with a Nikon D850 at 25 FPS (PAL) and 1920x1080 the result was H264 we converted everything to PRORES 244. Some shooting was at 50fps for "creative reasons" (maybe 26 files total).
We recorded the sound on a separated Audio Recorder at kHz 44800 and 24bit. Each recorded file was MONO, while the Audio from the camera was STEREO.
We made a 120 minutes feature, hence we had thousand of files we did a first editing using Premiere 2015 and the sound from the NIKON.
It made sense as synching all the mono files with their correspondent video was an endless job probably useless at this stage.
We needed a first cut in case we needed additional filming, or additional sound recording.
We created 1 hard drive with the following folders: Video (which included the sound from the camera), Audio (from the MONO quality sound recording), Animation (for some soundless animated files, timelapses and other stuff. These files have NO AUDIO), Projects (with the various Premiere prproj files), STILLS (for still images).
We copied the Video Files from the camera SIM CARD (Sony Super best quality) and the Audio Files with the USB connector from the recorder to the IMAC.
After the first work cut we added whatever we needed in the corresponding folders to the original external drive we work on.
With Carbon Copy clone a backup copy on a second drive which we backup daily.
Premiere came out with the 2017 version, we upgraded and saved the 2017 prproj-files in a new folder called 2017. In this folder we only kept the converted projects, leaving every other folder and files where they were.
We exported on a text file the various files we used in the Working first cut which were PRORES 244 25 fps and very few 50 fps.
This file told us which original file needed to synch with the good quality Sound files.
With Audacity we converted all necessary Mono Audio files to Stereo.
With Red Giant PluralEyes we created synched files using the PRORES video files and the Now STEREO sound files.
We saved in a new Folder called FILES (where we kept the new STEREO files created with PluralEyes in use in the project).
On Premiere 2017 we linked everything no problems.
Meanwhile Apple came up with an update and we updated the System.
After the System update we used Disk Warrior USB stick as a startup, and checked the directories in every drive we used.
Premiere came up with two updates since and we created each time new folders for the projects.
Before doing so we saved each folder as XML so now we had two DRIVES cloned exactly with Carbon Copy Cloner, with the directories fixed with DISKWARRIOR.
At this point we the first 2018 update me being to have link problems. as such:
After the error we flagged the files as offline and then we checked them with various utilities: they were exactly as they should have been both in the video (PRORES 244 PAL, and the audio. The 2017 projects opened again perfectly without any problems using the Premiere 2017 we worked with.
Of course since those versions, we had changes, additional files and more, so this was only a test to compare how the different versions worked. 2017 was fine 2018 was never.
Still the 2018 version promised improvements and functions which in theory seemed very useful. We decided to go for it.
As not very file linked back, out of desperation, instead of Linking back we used REPLACE File instead, always using the file Ver 2018 didn't like. The files worked perfectly, however many and randomly were no longer Stereo but Mono again and certain videos had vertical strips here and there.
In linking and Replacing we were particularly careful to choose the proper folder and the proper files. The error is a total mystery to me.
After replacing the projects worked, at times we would attempt to replace again to get the stereo files back, and randomly the stereo came back.
The exact same problem happened with the latest PREMIERE update. ONly this time the unlincable files were more and the time to replace was longer. The vertical stripes on the video where more.
We used Disk Utility to fix the system, DiskWarrior for the directories, and checked the FILES folder to make sure everything was there in order and fine as Prores 244 and stereo kHz 448000 at 24 bits. More hours wasted.
What am I doing wrong? Where is the catch? The system perhaps? The way the various projects convert from a version to next?
Thanks for your time if you will be patient enough to read this all. I wasn't born in english hence I write using my european mind ...so, sorry for any redundancy.
But please accept an additional remark.
I've been using Apple computers since the MACINTOSH 128. Since I bought probably 50 Machines. The last fully working machine I used without any problems was a MACPRO 4.1, and the last super best software which never gave me any problems was TIGER for intel and his various updates although each update had little problems. The last almost fully working System was Snow Leopard.
All the Mountain Systems are and were crap, updated so frequently that I wonder if they run out of programmers and have no time to fully check what they do. I understand the Iphone is the priority for Apple computers now, and desktop machines are just something from the past. I rented a round MACPRO but compared to my previous is really a toy. They are a company and they need to keep their share holders happy. They never particularly cared for users, but now they are definitively user hostile. Just for fun: My Machitosh ][ still only has 128 colours, but it works fine ... why?
I am a very experienced user. I know and used plenty of different software from various software houses. Each program as an undertext which can be very useful although perhaps design for reasons with nothing to do with the various aspect of the cinema world. As a film maker I need to use text for writing, Paint-Draw and 3D software for images, I used FinalCut 7 until they changed it in the middle of an important job and this was when I turned to Premiere.
I understand the system, its mysteries, hidden files and more.
I don't understand bugs .... I am 72 yrs old and I have no interest or time to learn programming and so on.
All I know is I had to relearn how to use my machines each time a new system came out. This as the MOUNTAIN system appeared and the Lions Systems vanished.
My beloved and perfect MACPRO died on me, and my very good Apple Store told me it wasn't possible to understand what was gone: the power? the board? They are experienced and they fixed machines which Apple told me they were not fixable.
So this is what comes to mind, and somehow I understand how thought it might be for Adobe to follow each new version of the Macintosh System Software.
Still I hope to be able to finish my film which took 2 years to make.
Regards and thanks
This is the error, and as I said in my far too long post I can REPLACE rather than Link back certain files
This error in the image refers to audio, but I also get similar errors telling me the video does not match
and other even more frightening errors telling me if I link the file the video will vanish and the audio part will be kept with the newly liked file.
Thanks again but really I will try to go back to 2017 and use the projects created with that Version and use my memory for whichever changes I did
The major result is that I will need to tell certain festival I am not able to submit the film and for this I can only blame ADOBE as the constant upgrades they give simply mean they don't have enough well trained people to check their work and use the users as tester
When Premiere gives me the errors I posted before 
and refuses to link the file to the project I tried just as a way out to REPLACE the off-line file but I always replace it with the very same one which originally Premiere refused to link
The same file, in the same folder of the same disk so there are no differences between the file which doesn't link and the file I replace the "offline" one. Is the same file
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