Zemlin,
I'd suggest running your notch filtering before you upsample the files.
Think about it... by upsampling a file from 44kHz to 96kHz, you're not actually going to introduce any frequency information above 22050Hz anyway, so filtering before upsampling will still result in the same end result.
On top of which, filtering the 96kHz files will just take 2.17 times as long to achieve the same result!
I'm guessing you're mastering stuff for DVD (?), but anyway you look at it, the files aren't going to be improved by upsampling. Therefore, you may as well do all your "restoration/turd polishing" at 44kHz and only jump to 96kHz when you're ready to compile the master.
Unless I'm missing something...