LR copying files to wrong folders and not always importing photos to catalog?

I've lately had very strange issues with LR.

Background info:
I'm using Lightroom Classic 9.2 on OSX 10.15.3. I've always used the LR default import folder structure of YEAR/CAPTURE-DATE. There are currently 33600 shots on the hard drive and some 100000 more in the catalog on a detachable archive drive.

Problem 1:
I noticed I'm missing some random iPhone photos from the catalog here and there. I'd synced them through LR Mobile.

Problem 2:
Deciding to try to fix the issue manually, I copied the files to my laptop through Apple Image Capture, and started the import. I had 12500 photos, and since most of them were in the catalog, I checked "Do not import suspected duplicates" - and ended up getting 11700 new photos. Obviously most of those were new duplicates.

Problem 3:
During the import, I ended up having random photos from (for example) December 2019 copied to May 2017 folders and imported into the May 2017 catalog. I only spotted the ones I was actively looking for, this issue could be very widespread since the one particular shot I was checking happened to be affected.

Problem 4:
Some of the missing May 2017 photos were also copied to the December 2019 folder, but were not imported to the catalog. Still the particular shot I was looking for was affected.

Problem 5:
It looks like some photos have swapped places, but there are also some folders that have a huge pile of photos from a number of wrong dates.

Problem 6:

Over the years LR mobile has created a number of duplicates into the catalog through sync, to the extent I had six instances of some shots. With the new import now I have even more duplicates.

I've used LR ever since the first version and have loved it. Now with this mess I'm getting desperate. All of my photos and edits from over the years are in LR. What can I do?