Teams Project with multiple Project bin files

Hoping to get some useful insight and assistance to an on going issue while using Teams.

I inherited a Production project with multiple Project bin folders that all have sequences and assets related to that particular project. To be transparent, there are 18 project folder bins not including project bin folders that are duplicated or copied, 

I have to mention I'm on a server where all of this media is stored.

I've tried to convert from Production to Teams to create a better workflow but when I open one of the new project bin folders, assets are created (all related to this particular folder). The conver went well except to discover some of the media was actually missing from some sequences..not offline but missing clips. This has caused days of delay.  I eventually dumped all of the footage from the server to a external drive in hopes I can avoid additional issues...nope, the same thing happens again. I hear teams can't handle multiple Project bin folders with stored assets.

Connecting proxies has been a nightmare. I want to delete old Teams Project but I'm afraid of losing so much work.

Hope this makes sense and even more hopefully someone can help.