I had a similar problem with my second batch last year. My autosiphon kept losing the siphon (where the hose connects to racking cane). The beer in the line kept gurgling (sp?) and I had to restart the siphon probably 3 or 4 times. The beer turned out just fine. It was a tasty Pale Ale, the last bottle was about 6 months old and didn't show any ill effects of the process. The biggest concern with that is premature staling of the beer due to 02 exposure. Don't keep the beer around for a year and you'll likely be fine.
A side note, if you had the same problem as me, I fixed mine by buying 5/16" ID tubing instead of using the 3/8" ID tubing that came with my autosiphon. The 5/16" is a bit of a bitch to get on and off (generally run hot water over the end to losen it up a bit to get it off), but many batches later it is still working fine. My 3/8" got streched out after 1 batch and that's when my siphon keep leaking/being lost.