Hi JKK_924,
As per your description, first please allow me to explain the sync default behavior, by default, Microsoft OneDrive sync client app sync SharePoint online libraries in folders under your Windows “User” folder, for example: C:\Users*username\ and* When you sync your OneDrive library, your files are placed in a folder named “OneDrive @CompanyName”
As you mentioned, when you stopped the sync via go to OneDrive Settings and when you restarted the sync. The SharePoint library "BB for Documents" start syncing to a different location and based on my experience this is really abnormal behavior as you encounter.
And since you also mentioned, “And to complicate matters, I'm getting a sync error for a "Projects" folder under TDI Team” based on my test Please try my suggestion below and see if its help.( I tested and I can sync all other SharePoint document library under SharePoint in file explorer)
Go to OneDrive setting page> In the Account tab, select Unlink this PC first, **** then if your OneDrive sync client app is not up-to update you may first try to install the latest OneDrive sync client app via this link OneDrive release notes **** on your machine, And then Navigate to SharePoint library that want to sync and click Sync and check the outcomes.
I appreciate your understanding and stay safe!!
Best Regards
Waqas Muhammad