I'm not sure where the problem is, but in 1.16, the Package Recipe Encoder fails to save certain "big" recipes remotely (i.e. outside of singleplayer or LAN as the host). The confirmed one I've found so far is the Ultimate Singularity on FTB University 1.16 (modpack version 1.3.0). (Also the Creative Generator, but inserting that recipe can freeze your game - it only works for me in singleplayer with 10G of memory).