You might want to try adding an inductor wired in series with the bank of caps (like ZIMO recommends in their decoder manual where they show add-on keep-alive caps circuits) and see if they can then be programmed without disconnecting the caps. Something like Digikey parts 587-1628-1 or 495-1982-1.
Thanks Pete. This idea is worth investigating, they are inexpensive and small too, about the size of a cap. Although space is always an issue in n scale it should be possible in a good many installs to find a spot to put it.
Could also use something like a Soundtraxx 810058 Micro-Mini Connector soldered on one side of the cap bank and its associated wire so you could just mechanically disconnect when the need arises. Not as elegant a solution admittedly but an option none-the-less.