The gondola, inside its cyclo-olefin canopy, could be sterilised on the ground by running the UVC LEDs inside a mirrored chamber! That sterilises the outside of the gondola; its own canopy gets recontaminated during flight and then is resterilised by the LEDs as previously described.
Since the gondola canopy has to have a sampling port - an invagination to the gondola itself insiden if you will - effectively the gondola can be prepared and attached to the port on the canopy with the canopy inside out, which can then be turned right side out and invaginate the gondola within it!
But would cyclo-olefin take this much punishment? Who makes it anyway?
Oooh! We could have a reusable balloon? Instead of bursting it we could incorporate controllable valves? After all, we need to have our custom cyclo-olefin job made anyway...