Yes they do remain set after reconverting to ISO, & yes it can take a bit of time to figure out the right combination of flags to set doing it that way but there are guides you can find online which list the optimal settings so you should only need to set them once & for some games it's the only way to get them working. Yes there are quite a few that require you to use the various options for full compatibility otherwise they can be glitchy (black screens, in-game freezes, gamedata fails to install, can't save properly etc). You can set gamedata to install on an external drive instead of the internal in WebMAN Mod but it doesn't have the other options. ManaGunZ & MultiMan both allow these options to be set but I've never used Irisman so I'm unsure about that one.
Sorry, but where are those guides and are they up-to-date? How can flags be set on ManaGunZ?
EDIT: I'll delete multiMAN and start using IRISMAN. It seems between multiMAN and IRISMAN only the former can set flags but solely in folder format games (so, pressing the "Square" button in the games wasn't working since all my games are in the ISO one) and I don't know how to set flags on ManaGunZ so I'll delete it as well. I always convert folder format games to ISO on the PC before even copying them to my external HDD so setting flags with multiMAN would be useless since I wouldn't waste time converting them back to folder format, set flags on multiMAN and then convert them back to ISO on it or even not converting them to ISO on the PC, set flags on multiMAN and then convert them to folder format on it. Also, webMAN MOD always freezes my PS3.
EDIT 2: I bought an used PS3 since the previous stopped reading BRs, installed webMAN MOD and it hasn't been freezing my PS3 so maybe it was the previous PS3's HDD's fault. Anyway, I got used to IRISMAN so I uninstalled webMAN MOD again.
EDIT 3: I gave webMAN MOD a new chance and before reinstalling it I deleted IRISMAN. The "webMAN games" setting was empty with my external HDD connected to the PS3, which is odd. I disconnected it, restarted the PS3 and it was no longer empty. I installed prepISO, connect the external HDD to the PS3 (the "webMAN games" setting is no longer empty) and use prepISO to scan the external HDD every time I make changes to my PS1 and PS3 games in the external HDD (which are now in the same partition, since when I was using IRISMAN I wanted to be able to toggle between the PS1 emulators and I couldn't do that if running PS1 games from the external HDD's NTFS partition where my PS3 games were but only if running the PS1 games from the external HDD's FAT32 partition [and it had to be the first external HDD partition, because if not, the PS1 games weren't even found]) since the external HDD is formatted as NTFS (also, IIRC, even after using prepISO, it wasn't reflecting the changes I made to the PS1 and PS3 games in the external HDD when it had two partitions [a FAT32 one for PS1 games and a NTFS one for PS3 ones] but it does after putting them in a single NTFS one).
EDIT 4: There's
multiMAN MOD which supports exFAT and NTFS unlike multiMAN.