The reason that I ask is because this is happening to LiDAR, and I am inclined to use lidar because it is easier to read.
As Wikipedia points out, probably the best rule of thumb is "can you speak it as a single word?". For instance, Nato (Nay-to) and Unicef (You-Ni-Cef), but USA (You-Ess-Ay) and FBI (Eff-Bee-Aye). Another common rule seems to be that anything less than five letters (NATO, FBI) can be capitalized all the way through, but anything longer than that (Unicef, Unesco) shouldn't, just because it looks ugly as full caps, although you can use small caps to make that look less ugly.
Personally, I think you should go with whatever your target audience is expecting.
I would assume acronyms lose their capitals once they become familiar and enter the English language as a standard word (laser, modem, ...)
Others won't be so quick to uses lowercase, like AIDS: