File System Publish Not Overwriting Replaced Existing Baggage

My team recently upgraded from 2017 to 2020. We have 5 sites we maintain and several thousand assets. We were unable to keep any of our baggage files (for now) in the assets folder to avoid link breaking (we were given 1 business day and a weekend for the transition and there wasn't time for me to get thousands of links to other PDFs out of existing PDFs, obviously the system update its own cross references but the PDFs with cross links are not the same situation - the baggage files we import are maintained by 10-20 different teams). In 2017 we had some PDFs baggage at the root level which I had to pull in to the top level topic folder with most of it being in sub folders. 

We currently publish to a File System. When we publish, RH is failing to pick up any replacement PDFs (we do 50-200 a week). It will pick up new PDFs, and page changes but no file overwrites are carrying over. We import any overwrites by right clicking on the folder it is in and selecting Import. We have been forced to change the publish settings to "re/publish all" for the changes to go - this is much much much more time (we publish all day long, it's 5 sites with 10 merged projects build tagged out to the appropriate of the 5 - four developers). The overwritten files DO appear in the generated help but are completely ignored on publish.

Any thoughts on the issue? This all worked perfectly in 2017. I'm not sure if we are uploading the baggage in the best manner, or if it is some server side setting (or a general failure in having a File System publish instead of something fancier). 

We are currently redesigning and rebuilding our projects so if I can't save myself from whatever is occurring now, I am hoping to prevent having to republish all in the future.