This is on purpose - I have changed the behavior because I think it’s better this way.
In particular, if - after deleting the virus from the archive - only an “empty archive” would be left, the whole archive is deleted instead. There is no point in keeping an empty ZIP or RAR file (a 20-30 bytes header in fact). The main reason for that were ZIPped viruses in e-mails - it’s better to remove the attachment completely than to keep an empty ZIP inside.
Of course, if you put more files into the archive, the uninfected ones will be left inside. There are also other limits (bigger files, such as SFX archives, won’t be deleted as whole). The behavior is not limited to Explorer-extension, the other scanners (Simple, Enhanced, …) should work the same.

Or, are you saying that the whole archive is deleted even when there are other (clean) files inside?