Deleting measures at start completely confuses MuseScore, all measures become anacrusis
Windows Vista Ultimate 32bit, MuseScore 0.9.4, revision 1753
Create a score (6/8 time signature) with 5 rest measures, enable and disable multimeasure rests, put only one eigth note at the end of measure 6, then type 20 bars or so of music.
Change your mind and decide that bar 6 should be an anachrusis (up beat), delete all 5 initial bars, change the now first bar to be an irregular bar of duration 2/8, all other measures become 2/8.
Score irrecoverable (as MuseScore tries to "help" by garbling the music when you attempt to fix all bars to be normal 6/8), have to retype all music.