I think that rather than a big portion of the Imperial forces just disappearing overnight, it would be more interesting (and realistic) to have something like the following occur: the Imperial player must move a certain number of forces to Trente, Austria, by a certain date (for example, October 1629). These forces will be then transported to Pavia (where there is a depot to avoid starving the locked forces).
If the player does not put enough forces there, some bad diplomatic event occurs that the Imperial player then has to live with. This way the Imperial player has to make strategic decisions about who to send and who to leave behind. There could also be a random factor such that sending more than the minimum increases the chance of a favorable outcome in Mantua.
RUS Gold has a mechanism where the Reds need a certain number of elements in the Ukraine in order to get rid of Makhno. The Imperials might need to put a certain number of elements in Trente to stop the NM from dropping every turn. This way of doing it would also eliminate the occasions where too much of the Imperial forces are taken away.
TYW is a great game, by the way, although facing 80%+ of my forces disappearing like this (as just happened) does decrease its appeal for me.