Yes, it is very unfortunate that the anti-virus companies do this. As a typical user, it’s very hard to see the difference and understand the consequence of allowing what is essentially a man-in-the-middle attack.
The way AxCrypt (and encryption in general) works, if a password has been compromised all data encrypted under the compromised password should be treated as potentially compromised. With AxCrypt you can indeed change the password, but the original password used when the file was encrypted remains also valid.
So, what you need to do is to re-encrypt (decrypt + encrypt) the files that you really would like to re-assert security for.