"Remove Unused" function seems to break Team Projects (at least between Premiere and AE)

Hello! I'm fairly new to the Team Projects workflow and I loved it when using Premiere Pro. Haven't had any major problems with it. However, I encountered some major issues when doing Team Projects between Premiere Pro and After Effects. Here's what I did:

1. I made a Premiere text layer an AE composition using the "replace with AE composition" function (which is how I have been doing it for years).
2. Then in AE made a white block then made it move around
3. Went back to Premiere and saw that the AE composition and the white block are now part of the Team Project library. I also noticed that the composition was labeled as "video used 1 time" while the white solid was not being used.
4. Did "remove unused" in Premiere and it removed the white block from the Team Project library even if it was being used in AE. This resulted in deleting the white block in AE effectively destroying the composition that I was using in Premiere.

So if I understand it correctly, a Team Project is a shared project library that the different programs like Premiere and After Effects has access to - even seeing files and sequences that the specific program is not using (Premiere having access to a shape object that was using in an AE composition for example). Manually deleting this AE shape object in Premiere will give a notification saying I should delete it in AE instead but with the "remove unused" function, it goes ahead and deletes it. 

I also tried it in AE as it sees the Team Project. Doing "Dependencies > Remove Unused Footage" deleted the files in premiere from sequences, audio, photos, etc. effectively destroying the whole project (ouch). So with Team Project, the "Remove Unused Footage" is not only useless but dangerous as it will surely ruin the project.

My question is, what am I doing wrong and how is a linked Premiere-AE Team Project workflow supposed to be? Am I not supposed to do the "replace with AE composition" function and instead use .mov exports from AE which are imported in Premiere? (just like the tutorial video (97) Video Masterclass | Collaboration Workflows with Premiere & After Effects - YouTube).

How do you do it? Thank you!