Hi Julie,
megreg is only used in imported data, not in raw files, right?
In the case of imported data, the Projectors have been already applied in to the data, and they are saved in each individual (run) channel file just to keep track of the what was applied. We made a recent update, now when the shared channel option is selected, the Projector filed is cleared in the shared channel, and there will not be warning, as it does not apply.
Best,
Raymundo