I am currently porting a game from version 2.1 to 3.2 of cocos2d. We have over 3600 pvr.gz files that are NOT flipped, eg were produced and working under 2.1. We tested out with
ok, many thanks to Scott Lembcke of cocos2d for pointing me in the right direction. For posterity, hope this helps someone out there. PVRTexToolCLI did the job for me (from ImgTech.com). Free to download, free to use, you must register on their site.
here is the syntax (for this game's assets strategy)
PVRTexToolCLI -i old_magie_cleanse-hd.pvr -o magie_cleanse-hd.pvr -flip y,flag -f r8g8b8a8 -legacypvr
notes :