Removing that folder is not the problem. In fact, is what the updater does automatically on each run, to clear the airport and models cache so, it's a folder that is SUPPOSED to be removable.
I would be more worried, instead, why the updater couldn't remove it. This can be either caused by the antivirus ( most likely ), but if the antivirus is interfering, you can't be sure of anything the updater did, or even if the program would even start.
So, before doing anything else, configure the antivirus to exclude the whole Addon Manager folder.
If that doesn't fix it, try running the updater after a Windows restart and be sure you don't get that message anymore and the updater completes successfully.