I used Amethystine Essence on a purple crystal of mine whcih only had one charge left. It added a charge to the crystal for a total of 2, but the 2-charge option of "Lesser Restoration" still wasn't usable.

Did it stay this way after a reset or two?

Not sure, it was a few weeks ago now and now I've used it for the healing.

I'm quite sure that I tried the restoration several times, even after there had been a server reset.

I'm up as a testpilot to see if it doesn't work with another, if you'ld like.