IMR is generally considered to be the safest chemistry. That doesn't mean they are 100% safe, just that they are widely considered to be a safer choice.
I use two AW IMR 18490 in an elzetta charlie that's been bored for rechargeables. I used to have six of them. Meaning, over the last five years, four of my 18490's have been over discharged to the point that the protection circuit tripped.
In my experience, here's what happens:
If I use the light on and off, on and off, to the point where they are low, the batts come out of the light in a fairly equal state of charge. Within .1 or .2 volt of each other.
If i use the light steady on until the batts get low, that's when the one towards the negative end will come out with a much lower charge than the other. Half a volt difference, or worse. Or worst. The negative-side battery is charging the positive-side battery. I suppose that's one of the reasons Elzetta recommends only primary batteries.
My LUC-V4 charger has a "Zero voltage activation function" and can bring batteries back after the protection circuit has tripped, and I tried that twice, and it seemed to work both times, but I don't like to play around with that kind of thing, so I tossed them anyway. How do i know the protection circuit wasn't damaged, and will work again next time?
The best thing to do is don't let them get low. 3.5 volts is low enough to recharge.
18490's are somewhat rare. Some "reputable dealers" had them in stock, but wanted ten bucks each. I found somebody on eBay that sold me four of IMREN brand for $19, free shipping. So far they seem OK.
Interestingly, when I first got the Elzetta Charlie, it's tube was not yet bored for 18xxx cells, and I tried using three 16340's. The third one in series (the batt on the negative end) came out dead every time. So, three is worse than two. The third one was charging both of the others.
I see several brands of IMR 16340 on eBay.... Fenix, Olight, among others.
And I see A123's for 1.10 each if you buy 50. That will solve all your problems. They are supposed to have extremely long shelf life.