Yeah. Kind of was a little surprised when it did that myself, and even more surprised when it seemed like I've been the only one to have this issue. Was a pain to figure out where it was the first time, but the second time (today) was much smoother, although still a bit of a pain.
One thing that I'm wondering about is if during the installs of equo or spritz it checks each of the individual links to see if they're still active, and removes them if they aren't. If that's the case, then this issue might be caused by some slight meddling from my ISP, as the last couple of weeks they've had quite a few HTTP/SSH brownouts, while other types of packets like UDP or torrent packets still get through just fine (which to me suggests that they're attempting some type of packet filtering, but are failing to understand that they're targeting the wrong traffic). However, I won't be dealing with them anymore in a week, as I'll be moving (also, they were the only option for my apartment complex, and no, they aren't Comcast, as it's an apartment run ISP).
If this is the real problem, then my suggestion would be to just accept repositories.conf as-is without checking, so that they don't get accidentally removed during the install process if the net connection drops (or in this case, is unresponsive).