I did the same thing the other day on my S3. I went and downloaded CWM and then used the messed up TWRP to flash CWM. Everything turned out fine with my S3 so you might try that. Something is really screwed up with Goo cause after I installed TWRP with it it was showing folders I had deleted before I even downloaded TWRP.
Also something else that may be safer, couldn't you just use Casual to re flash TWRP and then download the latest flashable TWRP version and flash it?
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