As i recall that's exactly what i did. I was having screen issues after i flashed different kernels, so i wanted to go back to the original backup i did when first flashed Myn's RLS3 (i backed it up with ROM Manager/ClockWorkMod). When i made the backup, i then renamed the folder/file using Astro. After the kernels messed up on me, i rebooted to recovery and tried to restore to that backup but was getting "file not found", which i assume was due to the name change. So i decided to troubleshoot the kernel flash by loading up RA recovery and doing the cache/dalvik wipes there. Wipes went fine, but after a reboot the screen was still messed up. I then booted back into recovery (still RA) and was able to browse to my original Myn's backup and it worked that time.
I was told that if a backup was made using ROM Manager then ROM Manager/ClockwordMod was the only recover that would recover it, but not in my case. I'm still using RA Recovery simply because it could restore what ClockWorkMod couldn't. I even did another backup, but this time used the backup feature in RA Recovery vs ROM Manager.
I didn't know it was dangerous to do, thanks for that info! I just figured they both backed up and restored the same, just one more stable than the other. I'm certainly using the backup feature built into RA Recovery from now on though, wipes and restores seem to work better.