If you are going to empty them into a carboy make sure you pour down the side to minimize oxygen exposure. I tried this once and while the beer wasn't ruined, it didn't quite have the same flavor as earlier batches.
I had a brew buddy bottle 5 gallons that had sat for at least 3 months in his secondary. After bottling it never did carbonate. What we did on his case was crack open the bottles and add a SMALL pinch of dry yeast (no more than ten little granules). After recapping he let them condition for a few weeks. This worked beautifully. I had tasted one prior to this and wasn't able to really tell a difference after.
A woman drove me to drink and I didn't even have the decency to thank her.
Kegged: Russian Imperial Stout - Belgian Dark Strong - Vanilla Mead - American/Belgian Ale