I'm using EE 2.8.1 and I just updated Wygwam from 3.3.1 to 3.3.3 by copying over system/expressionengine/third_party/wygwam and theme/third_party/wygwam folder contents over, then running "run module updates"
Everything seems to work, but my icons are all messed up. For example, the icon that is clearly for unlinking (the chain with the x on it) is now the icon for linking. And the one for unlinking looks like bullet points. And the one for inserting a "read more" break in the text looks like the text unformatting icon (the T with an x at the bottom).
I didn't know what to do so I restored my OLD themes/third_party/wygwam folder from a backup, and now everything looks okay. But I kept the changes I had made on the system/ folder. Ideally I wouldn't want to keep it this way, since the themes folder is the old version... but it seems to be working... but maybe there are some undetected problems from doing it this way. Any help or suggestions?