You're right, Flex won't work on a track with an active Melodyne plug-in, because what you're hearing is not the original Region[s] but a special wav file created when you Transfer the track [or sections of it] into Melodyne. But it should work if you use Bounce in Place [File menu > Bounce > Track in Place] on the Melodyne'd track.
This works here:
- Process the track with Melodyne, until you're satisfied with it.
- Use Bounce in Place [as above], creating a new track.
- Enable Flex on the new track [assumedly all the other tracks are already Flex-enabled].
- Make sure to MUTE the original track, with the track Mute button -- it's not enough that the BiP operation mutes the original Region[s], because, as I said, the Melodyne track is not actually playing that Region, it's playing a separate wav file that was created when you Transferred the audio into the Melodyne plug-in; if you don't Mute the Track, you'll still hear that Melodyne file playing back out-of-time at the original tempo.
- Enable Flex & Follow for all Regions.
- Adjust the Tempo -- all Regions should follow, including the new Bounced [bip] Region from the Melodyne track.