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Unprotected cells are better if you need higher current and they are shorter so they fit most flashlights.
Protected cells are longer so you need to check if they fit in your lights, but they are more foolproof because of shortcircuit and overdischarge protection. Their max. discharge current is limited by the protection circuit, often to less than the cell continuos discharge rating, so they can’t be used in high current flashlights like the Emissar (or any other light that would burn your pockets if turned on accidentaly)
The best cells for most flashlights are the Panasonic/Sanyo 18650GA and the Samsung 35E. The LG MJ1 is only slightly worse, so it’s a good choice if cheaper.
IMHO a good price/quality tradeoff for protected cells would be the protected MJ1 at Illumn if they fit your lights, you can get them at $6.50 + shipping. Zeroair tested their current limit and found it’s more like 7A than the 8A stated, but that’s enough for most lights.
You can get protected cells with a better current rating at Mtn Electronics or Liion Wholesale for about $2 more.
Edit: please don’t measure your current batteries with a metal caliper because it would shortcircuit them.