It's a bit buggy I agree
I had a file named Patch 3.0. I then saved it as Patch 3.1 and Patch 3.2. I closed opened Axoloti and both were there in the recent menu. So maybe it only saves the recent menu if more than one entry have been done to it?
I agree there is an issue there, but I never noticed it before, to be honest. When I work on a patch i often save many versions, so didn't really notice it. But it is a bit inconsistent.
I don't have a lot of hope that this is something that will be fixed for this version. Maybe version 2.0 will include it if you file it as a bug on Github. But yeah, that version 2, needs A LOT of work before it is usable. I tried it but basically no patch I opened worked. Only patches created in V2.0 worked. So I won't put any hopes up for V2 working anytime soon.