Not certain if this is the cause for your loss, but some of the earlier versions of Trainz will let you run the program, but if it isn't registered, it won't remember anything that you save.
Did you back up all custom content on an external source? I can't stress enough how vital it is to back up everything. Luckily, Trainz has a built-in backup folder you can use to restore your stuff. I lost 1000s of hours worth of content over the years, and backups will save you in the long run.
Ok, i checked again today, and actually it worked, but my custom content are not cloned anymore and they have now th same names as assets from which these were cloned