This does worry me a bit. I did some experimenting:
Deleting the file doesn't break anything.
However, if you delete the file to erase tracks and then run another application (be it a game or homebrew), the whole playlog is recreated, so it means there's another copy, possibly in RAM.
If you delete the file and reboot the Vita then play a 'real' game, when you enter the shell you will see only that game you played (so the list previously in RAM is gone after rebooting.) MLCL0001, which is MolecularShell, didn't show up in the playlog until I closed the shell and opened it again.
Here's how I experimented, using Retro City Rampage (PCSE00546 iirc) and Resogun (PCSA00137 iirc).
First: Run RCR and Resogun, and then shell to check the playlog - all three apps present. I deleted the log and then opened only RCR and then MolecularShell.
all three apps were present again (even though I did not open Resogun.)
Second: Run both games, then shell - all three apps present.
Deleted the playlog and rebooted, then only ran RCR and then MolecularShell.
Only those two apps were present, with Resogun missing
Third: Run several games (five tested), then shell. All of the apps are present.
Rebooted without deleting the playlog. Ran only one game (RCR) then MolecularShell. All of the apps are present.
Therefore, to fully wipe tracks you need to delete the playlog AND reboot the Vita. If you're gonna play legit games (especially online) I'd do this before opening the game. I don't know how the Vita uses the playlog, but for the time being I'll sign out the account if using homebrew, and perform a full wipe of the playlog and reboot before signing back in.
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