This is by far the most asked question in the past week or so regarding ss. I have spent many hours researching this question. Here's what I found:
1. Several in the s5 dev threads say yes it's fine to flash to stock and appear to have successfully done it with no problems.
2. Found posts from Scott, developer of clean Rom, and he does this on his note3. http://www.scottsroms.com/showthread.php?4988-Safestrap
3. Hashcode, creator of ss doesn't seem to recommend, but he did give us the ability to flash to the stock slot.
So there. Depends on who you ask I guess. Hope this helps.
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