Hi, I just came back from my trip and can confirm this. Permits for the Kyrgyz border are required both ways. On my way to Tajikistan I met a group of cyclists travelling the opposite direction who didn't know about this and had to wait 3 days at the border until their permits were sorted out. As per the message above, you don't get an actual permit, just confirmation that your name has been added to the list. I was provided with a reference number which seemed to help them find my entry but I met others who didn't have it and it was OK. I got mine from Ountravela, it was quick and efficient.
Good luck!
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