Whoohoo! Glad you seem to have found the culprit, looking forward to beta 2!
But please don't blame the Kuju union for this. After all, they are used to working on board the A/C equipped Dash 9s, or at least the SD40-2s, so I can see why it must've been a shock to be sent out working the FTs again.

No wonder they went on strike.

Quite an effective strike, too, if they managed to make entire locomotives vanish into thin air.
I've experienced some troubles with exporting, too. Though I must say, at this point I am by no means ruling out it's a stupid user error I am doing again and again.

I think that the 3DC export usually works if I select the Main object (or any RS-custom-field "wagon/engine" object in the first/main group) and then use the file menu exporter after one initial export with the plug-in menu train-sim wizard. I always say "yes" to the auto-LODs, and always "no" to the custom LODs.
Cheers!