I don't understand the problem.
A new model starts out with a default name of Model1.mdl
The first time you try to save that you have to do "Save As" and if there already is a Model1.mdl in the dir you are saving to you will get a warning.
Now, if you saved a model either with Save or Save As and got only a blank model file on the disk... that's a separate problem from this warning stuff, that's an outright bug some sort.
Just as a general note, I almost never save an MDL or an other asset separately. When I'm developing things I save entire PRJs with everything embedded and I never resave over a previous filename. That way my entire development environment is all in one file and if I need to go back to a previous version i don't have to worry that some change I made in a separately saved material or action or whatever will be loaded by that previous version of my project and make that older version of my project be not like the way it was before.
Disk space is cheap, it doesn't bother me that this everything-in-PRJs approach uses up a bit more.
If i later need to take a model or material to another project, I will save them out separately, just long enough to load them in the new PRJ and embed them. Then i'm back to saving whole environments again as PRJs.
For me, this is the safest workflow and I haven't had any saving mishaps or confusion with it.