No, Shared files are modified by interacting with the Ajax client. If you open a QVW with QlikView Desktop, reload it (or using the QMC) and save it will not modify its Shared file.

And to your previous questions, again, backing them up will depend on their contents and their criticality. I would argue that user created bookmarks must be backed up since they can be very easily recreated. Same with enabling Session Recovery.

However, if users are creating their own sheets and objects, backing up the Shared files is something to consider, bearing in mind that, generally speaking, a Shared file can only grow if it's not purged regularly using the qvs.exe tools mentioned in the links above.