PS3 Best way to clean up PS3 (filesystem-wise that is)

[Atari800]

Hi there team
Question #1:
I got a PS3 Phat and CFW 4.87.2.
I have been playing with Ultimate Toolbox 1.3 and 2.0 and PS3 4k 2.x and 5.0 - on top of each other and deinstalling/reinstalling those so I know I got a mess going on low level
I also tried copied some files into /dev/blind
I just used SEN Enabler to replace ConsoleID and PSID
*I couldn't find good documentation on this at the time
Anyways, once I put nw ID's in place, I could setup account on PSN but I guess I "zapped" all of my saves as most of the games either give some error about trophies or go to black screen and won't start
I tried using Apollo resign trophies and that didn't help
*I am guessing my new ID's probably is the culprit. But thats ok.

I know I can format the HDD and get that clean but what can I do about the flash? Does (re)applying PSUPDAT clean up flash?
I am just wondering if I should be worried if some FLASH gets filled up, will I brick?

Question #2:
Backing up trophies, game data, etc.....
If I create a script in linux could I just ftp over to the PS3 and copy files straight over or is it not that straight forward?
I was thinking of an incremental backup (copy files that change over time instead of a full copy)
I was reading about resigning files and what-not but if I were to place the files back to where the came from, I'd "think" it would be pretty safe? Right?

 

[Berion]

Saves and trophies are tied to user NP Account ID and encrypted by IDPS. If You changed one of them or both, You will no longer are owner and need to resign all of ps3 saves and trophies. Apollo do the job if You know how to use it. :P

Reinstalling fw is sufficient to wipe changes on flash. You don't have access to NOR, dev_flashes are on HDD in VFLASH partition. I don't know what will happen if You fill up eFlash on NAND.

You can backup and restore any files by any means but FTP server is not stable on PS3. I do not recommending using it for user backup data purposes. Go to tutorial section and read my tutorial Ultimate User Backup.