[SPOILERS]
I'm currently having an issues where a player on our private server isn't able to do "Lumen Harnessing" or get the progression "A...Less Than Honorable Attempt" he has done "A Less than honorable attempt" once already but it reverted back to being hidden behind cryptic runes again. I lead him to villager made ChC constructions, at least 2, and had him open the chests under them to try and get it again with no success. but in any case, i need the command to give him "A...Less Than Honorable Attempt" progression. Sitting here re-reading this i realized that we actually can't wait for the Tier 4 Pylon casting table because we need Repeaters for the casting complex... which is gated by our current problem.
it reset my entire book where i had 120+ pages, reset all progressions and all pictures in my Chromatic Lexicon had black circles with white question marks on them. It gave me all the starting books from RotaryCraft, Electricraft, ReactorCraft, and another Chromatic Lexicon too. I did not die or anything to have this happen and the gamerule keep inventory is turned on on the server as well. The server crashed shortly after and everything reset to a backup and fixed everything though, but this also happened again when i had 229 pages in my Lexicon getting sent back to the overworld from the Volatile Chroma Dimension by a Flare in the Far Lands, i had nothing appear under the recovery tab in the Lexicon either.
Have you checked their progress using "/chromaprog PLAYERNAME debug progress" or "/chromaprog PLAYERNAME debug all"
the person running this has to be in creative/gamemode 1. Try running "/chromaprog PLAYERNAME progress villagecasting true"