I would suppose you're fine, but the best thing would be to get a multimeter and check them just to be sure. I don't have that light or any cells that size, but I can't imagine they would have discharged that much further. When a battery is in use/draining and then you stop the drain, it will nearly always rebound a little bit. So, if you pull the battery at 3v when the light blinks to you, you may find that in a few minutes the cell has rebounded back up to 3.1v or something. Totally normal. Now, if the light is accurate and 3v is the blink, and then you leave it and there is some parasitic drain or something...then it continues to discharge a little, right? Probably only a small amount but what you may be seeing is the actual voltage cutoff in the light rather than the voltage warning. Warning gives you notice, cutoff shuts it down for protection. Maybe that's 2.8v or something (typical).
Even the cheapest cheap-o multimeters for $5 or whatever would be fine for this, so pick one up when you can...super simple to use and no risk when checking a battery. In the meantime, put it on the charger and just keep an eye on it. If it's getting very warm/hot, there may be a problem with it (i.e. warmer than it normally did before...some warmth is normal).
Keeping a cell discharged for a length of time is not good for its health (it may lose some capacity or cycle life) but it's generally not dangerous unless you're talking severely overdischarged where they're down at 2v or less for awhile. But...respect...so proceed and keep an eye on it...and get a multimeter when you can do so. (actually for the most part if you have a good smart charger that shows voltage that's almost good enough here...you can throw the battery in there and just see what it tells you...can always yank it back out before charging progresses if you want to. The advantage of the multimeter is that it will be a truth teller just in case the circuitry in the flashlight or the charger is not accurate/not the same.)
If it helps you relax any, the laboratory testing for many cells shows discharging (at a low rate) down to like 2.7v or sometimes 2.5v...this is usually how a cell's full capacity is measured by the manufacturers. They do that a lot in testing, and while we try not to go that low just for the sake of the cell's longevity/life cycles, it's not terribly harmful when it's for a brief period even if it sits for a bit before recharging. And remember, modern lithium-ion chemistries are much better than older ones, and different than the lithium-metal primary cells (like the CR123)...and generally using only one rather than two in series which complicates things. Pretty safe here, and when drivers have protection modes built in, it's much harder to get stupid or dangerous.