I try to switch my save to 2.1 and my last test ended with no train at all.
Alright, I did a basic migration test and checked all the locomotives and normal/fluid wagons. They all worked fine in my test going from factorio 2.0.77 to 2.1.12.
The simplest option is probably for you to send me the 2.0 version of the save. You can upload it to whatever works for you and give me a link. If you don't want to do this then I need a lot more information to try and work out what might be going on.
What exactly is disappearing? Locomotives? Wagons? What tier/mk are they? Is it whole trains? Are all trains from this mod disappearing?
What other mods might be affecting things? You can see the all the mods affecting a specific thing in the tooltip panel in blue text where it says something like Electric Train 2.0 Fix > some other mod.
If you want to properly test things then load up the save in 2.0, disable all mods other than this one, load the save and create a new manual save from it, then migrate that to 2.1. If that works then its some kind of mod compatibility issue.
Any other information you think might be relevant could also be helpful. If I cannot replicate the issue then it's nearly impossible for me to fix it.
I did go and look through the entire patch notes for 2.1 but the only relevant changes I could see are some new optional flags to do with the quality changes. Certainly nothing that should cause trains to disappear between versions.