As long as you have not overwritten your sequence, all the information should still be there. You just need to figure out how to fix your profile so that it will open correctly.
The error that you are getting is caused by a mismatch in the number of channels vixen is expecting and the number of channels in your profile. This is usually in the sort order section of the profile.
If there are more channels in the sequence than in the profile, vixen will simply cut off the extra channels. Once you save it, any data in those channels will be lost. If there are more channels in the profile than the sequence, the extra channels will simply be blank.
If you don't mind sending me your sequence and your profile, I can probably fix it for you (assuming you haven't written over it and still have the original sequence with all the channels in it).
Vixen saves the values for each cell. So the more channels you have the larger the file.