^ of course it does matter. it will determine the best way for you to do what you want to do given your situation. especially when it appears that there was a change in track muting specification in between os 4.71, which Prophecy is using, and the current 4.99B.
that being said, prophecy, i if there were no track mutes, the easiest way to do this with os1 w/ a song is to go through each seq and DELETE ALL NOTES on MUTED tracks so that it the song CONVERTS TO SEQUENCE without muting conflictions between sequences. unfortunately this is trickier with with recorded track mutes since they're an actual part of the song and it becomes difficult to tell them apart from simply MUTED tracks
why, do you ask, should i convert the sequences to a song? makes it way easier to resample
so here's what i advise you do, to avoid getting conflicted MUTED/AUTOMATED MUTE issues. please note that i tried this on 4.99B and it worked--but specification changed somewhere along the lines. odds are that it'll work though.
go through your sequences and observe your mutes, as they come and go. here's the important part: FOR TRACKS THAT STAY MUTED THE WHOLE TIME, hit ERASE and DELETE all NOTES. leave the track, though, don't delete the TRACK. do this for all sequences, but make sure you're only deleting notes on tracks that are muted the WHOLE WAY THRU the sequence - not ones that have recorded track mutes.
then convert this to a song, and play it back. make sure it worked: make sure that there are no weird mutings or missed "mute on/mute offs"
like i said, this worked on 4.99B.
now, solo individual tracks, and resample one at a time. if you have multiple sounds on a single track that need to be separated, you'll have to resample X times on that track. save the resamples one at a time (they should be the full length of your song) and do it again and again til you have everything
lengthy process, for sure. it's lengthy even if you have a sound interface, but not nearly as tiresome as the way i just described. still, it's the only way to do this via resampling.
your dude better thank you for this haha