More mundane solution - just because spells can't cross the window doesn't mean other stuff can't, once it's been located.

Instead of setting an ambush and waiting for their enemies to regain full power or completely flooding their home, the castle dwellers should force them to come out as soon as the ambush is set up. If a large fire is built under the window, all that smoke is going to go right into the PC's refuge. Guess how long before the air in that little extradimensional bubble is unbreathable? Things like flasks of flaming oil can be tossed in as well, just to speed up the process.

BTW, there's also no reason why folks can't just get a ladder and climb into te space themselves, once they know where it is.