As it already been said, check the method of transfer first.
Worse thing which can happen is that the game ask you for two A:\ or B:\ drives simultaneously... Which can most probably be bypassed by copying everything in a single folder and flagging it as A:\ or B:\.
If the game is good enough they'll even allow you to input the source and destination, in which case you should have no problem at all since you do have the power to mount whatever you want in DOSBox.
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