I came across this same problem today. I know this post is getting old, but hopefully this answer is useful to others who have the same problem.
To clear the cached HiRes Textures, navigate to: /home/pi/.cache/mupen64plus/cache/
delete the file: <ROM_Name>_HIRESTEXTURES.htc
Where <ROM_Name> is the name of the ROM you want to clear the cached textures.
Say for example you wanted to clear the high resolution textures for Super Mario 64,
rm /home/pi/.cache/mupen64plus/cache/"SUPER MARIO 64_HIRESTEXTURES.htc"
-LedHed