I've searched through the program for a way to do it, but if it exists, I haven't found it.

When using the Refresh Updated Profiles option, you cannot edit the profiles directly when previewing the changes.  I often find changes that I want part of (like fixing a typo in an actor's name), but the online profile would change part that I don't want (like overwriting any local common names).  So in order to incorporate the change, you need to close out that window, go find the profile, make the fix, then select Refresh Updated Profiles again (which means it needs to load all that data again - with a huge collection this can take a while).

What I would like is an option to either flag any profile that has an update or use the filter option to do so.  This way, I can either accept the change or make the change without all the hassle.

My Profile Comparison Plus (see this thread) allows you to flag a profile manually from the preview window. It also allows you to open the comparison preview in a new non-modal window, which means you can see the changes and edit the profile at the same time.

Please note that PCP has not yet been updated for DVDPro 3.5, but I'm working on it.

Besides that, I agree that a feature to automatically flag all profiles that have updates available would be a good idea. I'm currently using a self-written Update Manager to do that and some other things, but it would be nice to have it in DVDProfiler itself.