a. You can`t have damaged all the batteries. It is unlikely all be damaged, especially when you have two different chargers.
b. Even if they were damaged then they would not be limited to the same flying time. One would perform better than the other.
c. In such a case then one or more batteries would have already started to expand.

There is something wrong with your helicopters right now.
Maybe at the beginning you had a motor/3in1 failure, and maybe you had damaged one or a couple of batteries.
But since you got it right, you got 3x 2min flying time, now it can have gone to 2min by just the batteries.
Something is wrong.

1. Check the gear to pinion mesh -as already said, the shafts to be easily turned by hand (except of the magnets effect) so to check there is no bearing failure.
2. Check the blades. Any cut or bent blade is useless. Blades are better to be changed in pairs than just a single one. Of the same brand as the other rotor`s blades (all four blades the same brand). Better use stock blades for testing.
3. Check the flybar link rod adjustment, so the upper rotor blades have a nice tracking with no vibration at all.
4. Check for bent shafts. Any wobble or vibration is killing the power.

If still you find no problem then test the batteries themselves.
Remove all the blades and the flybar, connect a fully charged battery and run the helicopter at middle throttle, or a bit less, for 5 mins.
If it runs at the same speed then the battery/ies is OK.

And a quick question. Does it have the same lifting power as it had when "batteries" were "good"?