Hi again,
Thank you very much for providing the save - it really helped me trace the issue.
Unfortunately... well, I believe the issue is with the mod API. It sometimes doesn't inform my script about an entity, and it's essential that it does for it to work. You can find the full bug report here if you're curious: https://forums.factorio.com/viewtopic.php?f=7&t=78987
(I know you might not have used robots, but it was easiest for me to consistently reproduce when doing bulk construction).
Unfortunately, this means it probably won't be fixed until 0.18, as the devs have said there will be no more 0.17 releases unless they discover a critical issue. For now, the workaround is to deconstruct the siphon and reconstruct it. I'm sorry for the inconvenience of this.
Thanks again, and have fun.