Many thanks Norby & Cody!
Doh! - Don't know why I didn't see the save file, seems embarrassingly obvious now.
My save file contained this:
Not sure what the delay value is about, but stage-destroyed and substage-searching might explain something.
Wondered if re-setting COTBS_stage to the prior variable would trigger the re-spawning of the base. Didn't know what value I would need in there, so I tried exploring the program files in the OXZ.zip. In the Scripts folder / cotbs-main.js (I'm a Linux Mint user, so home/GNUstep/library/ApplicationSupport/Oolite/ManagedAddOns/oolite.oxp.cim.cotbs) I found reference to some of the game variables, so I guessed a bit and tried re-setting the variable COTBS_stage to PRESENT.
Possibly that did the trick because I subsequently found the base again. However, it wasn't in the place I was expecting and had been looking, so it's possible - but less likely - I'd just missed it all the time I'd been flying about.
>> V'q orra sylvat evtug va gb gur fhafcbg, ohg V ybpngrq vg nobhg (gjvpr) 400xz sebz gur fha / 1700xz sebz gur cynarg, ybbfryl va gur qverpgvba bs gur fhafcbg.. [translate at http://www.rot13.com/
After a couple of attempts I managed to take out the Asps - Jeez, they're vicious - and defences, but the base exploded of its own accord, and I couldn't find the transmitter among the rubble. However, after getting to a safe place in the system to fix up the damage, the Adversarial made another appearance. I checked the save file, and the mission variable was still at PRESENT. I managed to take him/her out again, got reinfected with the Curse, and after a stop at the next system to clean my ship up, went directly back to locate the base, which I discovered in roughly the same location as before. Managed to take out those fiendish guards again - despite the Curse leaving me severely limping throughout the battle, and the same thing happened, disappointingly - the base self-destructed and took the transmitter with it.
In my save file the mission variables have now progressed to COTBS_stage = DESTROYED + substage = SEARCHED, so I'm guessing I've now completed the main part of the mission, with just a hefty price tag to come.
Thought I'd share in case others found that helpful.
Relieved to have finally got it done. Many thanks again folks, and respect to Cim for a really hard and interesting Mission!