I had this happen to me also after several game days, the Xenon got to it in my case just before I was about to buy more XL Crystal Fabs, XL Cahoona, and XL Cattle [1 of each] for my weapons complexes.
- I ended up restoring from 4 savegames previous to latest - no great loss, just an evening - to just before the attack, and dropping an M2 with escorts into Akeela's Beacon - That took care of that!

It looks like the part of the challenge of XTM with Ashley's fabs is to provide additional security to various sectors - not just your own factories etc...

Also the pesky Xenon also took out Ianamus Zura's shipyard with two of my capped ships docked - but it has not respawned yet..??
Some general notes in sequence of X3 vanilla to X3 XTm with Ashley's fabs:
1. Initial vanilla game, after completing the vanilla plot I did Bala Gi...1st PHQ in Patriarch's Retreat.
2. Setup several complexes in Vanilla game - pre Ashley's mod ...talk about hard work!!
3. Used the X3 to X3 script to copy out vanilla savegame prior to XTM upgrade...good resources elsewhere on this site for this process!
4. Upgraded to XTM with ashley's fabs.
5. Ran X3X3 script again to read in savegame after doing a non plot start with a discovery and one trader. This added all factories [not as complexes] and my PHQ was supplied back to me in an additional Mammoth


6. Docked all Mercury UT's as they where being destroyed, purchased Terracorp Vulcans and used the pilot transfer process to place my UT's in the Vultures...only lost two in a dozen game days and gained $900 M credits regardless.
7. Relinked my factories into complexes..that Hyperion makes a great tug boat IMHO. Note that when adding to an extended hub you need to select the extended hub first otherwise the standard hub replaces it...
8. Added the enhanced version of the Trade Command Mark 3 software that allows sector locking so my UT's dont pillage or overstock my PHQ's...
9. Only done the first couple of XTM bullettin missions, as having too much fun elsewhere!! - was also offered and completed the Bala Gi missions a second time

10. I dont want to add any spoilers....but those pirates in certain locations are feral!
I have resisted the urge to add anything un-neccessary, the only other mod or script I am considering is the Anarkis Carrier Commands etc...
Thanks to the XTM crew for a great mod, likewise many thanks to Ashley for her great mod that makes the factory complexe business a lot less tedious. Also thanks to the rest of the mod space for their assistance.