Long time pkhex user since XY, and I've never had any issues until recently.
I edited a whole box, but when I saved it to my main save file none of it was there. I double checked that i was hitting "Set".
Happened again. Third time around,, I kept a Pkhex window open with all my edits - saved it but did not close it.
I then re-opened another window , loaded my newly saved main file, only to see my changes still didn't cross over again. I saved all my newly edited mons as pk8s and injected them manually and then it worked and saved. I usually edit the main file with no problems or saving pk8s, but lately have to double and triple check before uploading into Checkpoint.
The problems are not happening when editing Pokedex, bag items, money, BP. etc - That crosses over fine - only boxes are the issues.
Thank you for all your work and help....i know this version is still in its early Gen8 stages.
EDIT: I switched from using Checkpoint to Edizon and it works much better, as has been reported in this post. Checkpoint is glitchy.