Hi today while playing re:r the grey rubber fell.
I found out on ebay those:
1. http://www.ebay.com/itm/New-Analog-Controller-Joystick-Cap-3DS-XL-3DS-LL-/161300680360
2. http://www.ebay.com/itm/New-Analog-Controller-Joystick-Pad-for-3DS-XL-3DS-LL-/151269362704
Shall i buy both in order to...
You might upload a save file so someone can test it or wait for someone that has played the game to confirm this.
Also try to format to exFAT your microSD and try to copy the ROM again from another source.