What flash card? Most of the time you just have to reformat the mSD and put a new kernel on it.
Edit: just re-read the title, r4 clones should just need the above although I'd wait for confirmation on which kernel to use.
Also, I'd try backing up the SD card and trying known 'corrupt' games in an emulator, I know at least some newer games require newer kernels, if they are corrupt I'd suggest at a bare minimum formatting and testing the SD card with h2testw or perhaps looking to replace it as it could be a sign of failure.