if you removed repositories using UI then that might be the issue as there was a bug that manifests in exact way as you described. It happened when you had opened given repository project in authoring perspective and then you removed it. UI which keeps track of various editor actions did not properly handle that situation and thus NPE.
It should not impact your project from other repositories besides this error being shown.
It takes just over 30 seconds every time I switch to Authoring. I'm assuming that has something to do with all the errors. Only after that can I get any response from the error dialog.
By that time I've usually gone onto work on something else and by the time I come back I've forgotten what I was doing.
Is there something I can delete to tidy things up and reduce these errors?