So I’ve been able to replicate this, and here’s what happened, and how to avoid it (could be the same for you, or not).
I opened a Cubase project with a SV1 track. I went in to SV1 and saved the SV file to my desktop.
I added a SV2 track, loaded the SV1 file, and assigned an SV2 voice to it. I worked on it a bit, then saved my Cubase project file
[if you like suspense, skip this bit, because this is the key] I deleted my SV1 project file from my desktop.
I opened my Cubase project, and the SV file was gone, both from my SV2 track and from my SV1 track.
I exited Cubase again, retrieved my SV1 file from my trash, and put it back on the desktop. I opened Cubase again, and there it was - it appeared in both my SV1 track and my SV2 track.
I don’t really understand WHY this is happening, but obviously when I save and load files from and to Synth-V, it thinks I want to start working with external files, instead of the data being part of the Cubase file, which is how I normally work, and sure enough, under the File menu, there is an option to save to external file, or Save Inside Host.
So, to avoid the problem, after loading your SV1 file into SV2, go to File > Save Inside Host. For the purposes of integrity of your SV1 file, do the same in SV1.
Now its safe to delete the separate file from your desktop.
I consider this a bug, even though technically its a configuration issue. You can avoid it from happening, but it does require action when you’re converting files from v1 to v2, and thus saving and loading externally.