Unfortunately it's not my server, but I could easily test this.Look in the log file. Do you see something like this?
2019-01-01T11:44:20 1260.463 INF Vehicle vehicleBicycle_2579 out of world Kill
2019-01-01T11:44:20 1260.851 INF Entity 2718 killed.
Only instead of vehiclebicycle, it is whatever vehicle you are loosing. I get the same thing. I'm not sure what causes it, but when the chunk loads, it thinks the vehicle is out of the world, and it deletes it.