I hadn’t noticed this myself as I don’t really use custom sights however I just tested this now and I got the same message as you on the Dev client. It moved the “UserSights” directory with a couple of custom sights in it from my main “WarThunder” directory to the directory specified in the message. It also deleted the original “UserSights” directory as well.
So everything seems to have worked fine for me. I would imagine if your UserSights directory was a symlink that’s probably the issue.
Could you please submit a bug report regarding this issue so I can forward it?