Sure, but you could just over write everything on the old without needing deleting it first. I test that part pretty much every update to ensure it works properly, same with the update only patches. That's one of the reasons of using RPA's over loose files, everything that needs to be updated gets updated.meant trs2 update 6 aka 2.6. currently old and new share same folder name and if deletes old while copies new to where game resides then problems will arise.
Only time when issues of any sort usually arrives is when the script.rpa is unpacked and the rpy's and rpyc's are left behind. Well, that has been 99% of the cases, outside of random save breaking because I changed a period to comma or because solar flares or something, or ren'py deciding a variable isn't defined when it has been defined for 3 updates already. Still bitter about that random error. Anyway.
Besides update 6 is already on patron cycle so would be bit late for that But as said, I'll consider it in the future.
(Disclaimer: Haven't really slept properly in couple of days so take what I write with grain of salt. And chances are that I completely misunderstood things.)