I have disconnected these projects ( 3 projects that I found out where Linux only ) from BAM and I still cannot remove them from the Project Tab on the Advanced View console. Not sure what else if anything I need to do, please help.

First shut down your client.
You can find the projects files in var/lib/boinc-client

Remove the project files from that directory that are no longer needed. Restart the boinc manager, the projects that you did not want, and hard to remove should be gone. Only the projects you are still interested in should be there. There may be a better way of doing this, but it worked for me. Hope this resolves your issue.