The only remap I saw was for saves. Here is my runcommand.log file:
https://pastebin.com/7v67SJe0

the last line of the file (shown below) repeats well over a thousand times but I cut almost all of them out of the log file i put on pastebin for sanity's sake.
[libretro INFO] [MAME 2010] 'maincpu' (FFA649F0)[libretro INFO] [MAME 2010] (no context): unmapped program memory word write to 01D01070 = 0000 & FFFF

Thanks!

@mitu
you got right!
i start the MetalSlug game and there is it all be correct and works fine.
its only non co-op games there will only player1 work.

will try some other games and will see if all be work fine

thx

Open the options on the Retroarch menu and there's an option whose label I forget that will "map directions to digital" instead of analog. It's set to analog by default. I had to do it a few days ago.

See if it works.

Please add more info about your system, as detailed in https://retropie.org.uk/forum/topic/3/read-this-first.

@grimdanfango said in Location of joystick configuration files?:

Should the 2 files be the same?

No, they have a different syntax. But instead of bumping an old topic, please open a new topic and explain your problem, adding some info about your setup - as requested in https://retropie.org.uk/forum/topic/3/read-this-first.