Most protected cells use the same protection chip, which has a trip point of 2.4-2.5V. This is well below the manufacturer rated voltage of 2.75V. Repeated discharges to 2.5V will probably degrade your cells. The result will be lower capacity and increased internal resistance.
Charge em back up, they should be fine. I will note that protected Panasonic NCR18650B 3400mAh cells do not make a lot of sense. The fully charged voltage is 4.35V. The overcharge voltage of the protection chip is 4.25-4.30V. You would never be able to get a full charge in the batteries. On the plus side, cycle life span would be higher when not fully charging.
Edit: Crossed out apparently erroneous information. I looked for a Panasonic datasheet on panasonic.com and they list the cell with no datasheet.
Actually, the full charge for NCR18650B is 4.2v, I don’t know why so many people keep claiming it is 4.35v as that was a misprint by CNQG.
2.76v should be ok on the NCRs, even for regular discharges, as they are rated down to 2.5v. Many other brand cells don’t like to go below 2.75 or even 3 though.
Yes, NCR18650B are 4.2V down to 2.5V. Protection usually trips around 2.4V, if they had only 2.76V after 1 hour in the charger, they were really down to around 2.5V. They wont explode or really suffer from that, but doing that more often will let the cell age earlier.. the PCB is there to protect the cell, not to turn the light off.