Hi Lilikate! Glad you like it. I'm not sure what you mean by count the total number of tones? What exactly do you want to count, and for what reason?
If you output the song into multiple ABC files, they aren't guaranteed to line up exactly. Maestro removes silences greater than 1 bar's length before the first note of the output file. So if the parts in the second file don't begin until (say) 4 bars into the piece, then the second file will be out of sync with the first. I'd recommend you export the entire song into one file, and split it into multiple files later if necessary.