Hi Franck,
For the RAIN file: Have you tried to manually repair the file? (eos file adjustreplica <path>) It should recreate the failed stripe in another disk (and delete the bad one). If not, you can also try to drop the stripe manually eos file drop <path> <fsid_of_the_bad_stripe> and then run the eos file adjustreplica <path> to restore the file to the nominal number of stripes.
For the 3 bad files I think that you can just remove them from EOS namespace (the files will be lost) doing eos rm <path>.
And yes, finally the file system should be empty and you can proceed with the replacement.
I hope it helps,
Roberto