I don’t think I’ve seen any bikes go missing, but as you say its hard to tell since I don’t keep an inventory and I ride the same handful normally so wouldn’t notice if one of the others went missing maybe for months
I and a few others did have jerseys go missing recently though (see link below) so I do wonder if maybe its related and is a general bug.
Do the bikes show in drop shop now as unpurchased and available but at full/normal price? Or do they show as purchased in the dropshop but simple not in your garage?
I’m afraid that I don’t know enough/am not technical enough to know if there’s some kind of log you could use as evidence of the purchase. But one thing you might try as “evidence” for zwift is to check your activity list on the xwift feed and see if you can find any screenshots for rides you did on the Felt - that would be evidence that you did previously own it if that’s what Zwift are demanding. It would be a pain looking through them but might be your only option 
Here’s the link to the jersey thread just for reference: