Trapped air can hold back the water flow in a sealed pipe, I have had this happen. I would use a trash pump to try to suck water through from the outlet. Forcing water through from the inlet side will work if its air, but if it's debris it could become completely plugged. If you find that it was a high spot in the pipe with trapped air, it may come back. I had this problem of reoccurring trapped air. If the pipe is gravity fed you can put a breather line in the pipe at the high spot which will allow the air out. The breather just needs to be higher than the outlet so water does not come out the breather. This solved my problem. If the pipe is a siphon obviously you can't do that.
