Hello Hari,
Instead of deleting the average references from the projon ave.fif data structure, I tried disabling them(setting the active tag to 0) so as to keep the dimensionality the same. Do you think this could help? (In this case the resulting averages looked a little different from an alternate option of viewing the ave.fif originally set to --projoff but manually checking all but the average ref projectors On in mne_browse_raw.)
Best,
Candida