Sure, it's fine to add the caps yourself. However, since we can't vouch for the rework or parts, we won't be able to warranty the board(s) if they are damaged in the process.
If you want to proceed, you can stuff 3.3F 2.5V supercaps (e.g. Cooper B1020-2R5335) for C188 and C189.
Make sure that the charge/discharge components are populated on your systems (we usually stuff them, even when the supercaps aren't). Locations of the components on rev C BitsyX systems are shown below (they're probably the same locations as rev A). The component locations are in (X,Y) format in 1/1000 inch (mils) relative to the mounting hole at the corner of the BitsyX where J10 and J3 meet.
D20 (325, 1250) BOTTOM 1A Schottky diode (e.g Vishay Liteon or Diodes Inc B120)
R263 (575, 1250) BOTTOM 22 ohms
R309 (475, 1250) BOTTOM 22 ohms
R273 (175, 1375) BOTTOM 470k
R274 (175, 950) TOP 470k