IPad and IPhone - backing up "corrupted" file - spyware on IPad
It's kind of Catch 22, but with a get-out clause... 

If you let the Windows antivirus delete the suspect file, it will corrupt the backup.
However, as it is being recognised as a Windows virus by a Windows antivirus, then it almost certainly cannot actually have any effect on the iPad.  

The iPad, of course, does not run Windows &amp; cannot be infected by a Windows virus - even if it can 'carry' one &amp; unfortunately, possibly pass it on. 

One 'fix' would be to ensure your iTunes backups are encrypted [an option available in the Summary page in iTunes when your iPad is connected]  - that way the Windows antivirus can't even see the 'infection', nor, as the file would be encrypted &amp; unreadable by Windows itself, could it infect your PC.

The other - more long-term - fix would be to delete the offending files from your iPad; your next backup would then be clean.