Saving as a Copy to PDF flattens the layers on the original ai file and then copys the layers on-top

[Whimsical_Coconut8244]

Hi all, 

I am relativly new to illustrator so maybe im missing something obvious in the file saving settings,  but my work consists of importing a architectural drawings as pdfs, and adding various layers for different layers. The issue i keep running into is whenver i save my i file as a copy pdf it messes up the original ai file by flattening all the layers i have added hile also placing them on top of the drawing for a second time. is there a way to avoid this? i keep getting various messeges pop up about linked file changes when opeing the files to see these issues. 
I am saing my files on a shared google drivebut i am the only person working on the files. My thought process was to save the file im working on as the ai file and when im finished the first revisioon i will save a copy as a pdf for markup, but when returning to the ai file to edit after the first revision that is when the issue occurs. 
any advice is appreciated, thanks!

[Anna_Lander]

Hi,
do I understand you well? You Save a copy, and it changes your original file?
Could you please show the screenshots:
- the layer structure of any working file (the artboard is not necessary, just the Layers panel)
- the Save a copy window
- the Pdf settings window
- the layer structures of the PDF file and the original AI file after saving a copy.
Of course, it makes sense to create a copy of an original file (via Save As command) for experiments.
With the screenshots it might be possible to say something useful.

[Whimsical_Coconut8244]

Yes i save a copy of my illustrator file as a pdf, then when going back to my illustrator file a day or so later it has changed.
I have messed around with saving the file and pdf settings in hopes of fixing the issue with no luck as of yet. 

here is the current PDF screen

The layers stay the exact same, except all the layers of the original get flattened onto the first layer, while the other layers remain the same.

[Whimsical_Coconut8244]

Forgot to upload the save copy screen. here it is.

[Anna_Lander]

This looks strange and not clear :-(.
Please share one full set (for some less important image, copy, maybe without a part of image to be sure on copyright security):
1. AI copy of the original file (make sure that it is layered)
2. PDF file tha you created by Save a Copy command.
3. Original file that was created by the program, without your actions, during saving the PDF file.

It looks bizarre, maybe the files themself can help to understand what it is.

[Whimsical_Coconut8244]

I have found another issue which might make it more clear, i use the initial architet drawing for two different jobs,and saved it as seperate files for each. 
I have one with blue lines drawn as such 

and one with coloured sections as such 

i believe the issue may be to do with linked files as when opening my file with the blue lines today it has flattened the image with colours and use that as the "original" layer. shown below where it seems to combine the files. 

For some reason the linked file takes the copy i made and not the original document.

[Monika Gause]

Where do you save your file?

Does this also happen when you save as an AI file?

I do not think I understand what is happening to your layers.

[Whimsical_Coconut8244]

I save the files on a shared google drive, and yes it still annoyingly happens with ai files.
I think its something to do with the linked files but i cannot be sure.

My general work flow is as follows.
Get architect doc > Create 2 copies > Open each copy in Illustrator > one gets blue lines >one gets the colours > save as ai files while im working on them > save to pdf when first revisions are done > when i go back to the ai file again after creating pdf the issue happens

[Anna_Lander]

Please share a set of working files. You can put them on any file store (e.g., Google Drive, or any other that is good for you) and post the link here. The issue is quite complicated, and it's difficult to understand without seeing the working files.