No XLinks. The number of files is correct, but the number of merges is not, they are all unrelated. I have managed to work round this by shelving everything in the workspace and undoing all changes, then updating then unshelving, but this is a real chore. This occurs regardless of the number of files incoming - I have had the same behaviour with just a few updated files.
I'm having a recurring issue when updating my workspace. The incoming changes show no conflicts, but then all the incoming files seem to get dumped into pending changes. This leaves me with a pending changes tab with tens of thousands of changed files, which should have just been a straight overwrite. I have attached a screen capture of the aftermath of a typical update. There are over 70,000 changes files in these merges - the workspace had three changed files in pending before updating. Attempting to undo changes or otherwise interact with my workspace after this will often break the workspace such that operations spin for a few hours then spontaneously fail. This is obviously a massive workflow issue as it takes me hours or days longer than normal to do any sort of update.