Have not found this one in any of the bug FAQs or known bug lists.
CE, DOS version, via Dosbox 0.72 under XP SP 3.
Beginning of May. I detect a Battleship coming in to attack my #3 base (in China). Unfortunately it is defenseless; its first soldiers and Skyranger were purchased just before the end of April. I transfer out most everything, sell the rest.
When the base falls undefended MY #1 BASE ALSO DISAPPEARS at the same instant--or rather, it disappears from the map and loses all its personnel, aircraft, and stores. Clicking on it on the base screen shows it to be supposedly located in the same region as my #4 base but it cannot be found on the Geoscape. (Base screen also shows layout unchanged but facility count is wrong--same as the much smaller base #3 that was lost.)
I thought that this might be connected to all the stuff that was in transit from #3 to #4, so I tried again, this time selling everything instead of transferring. No change except that the nominal region of the missing base #1 is now that of #3 instead of #4.
I think that this must be somehow connected to the Skyranger and 12 soldiers who were pending delivery at base #3 when it fell.
Going back and not ordering them would be too awful--I would lose three missions that took 8 hours or so.
I read about replacing one data file with the version from another save in order to eliminate ufo's in flight but I am reluctant to try that for fear of making a worse mess.