It's either (a) you're not pasting the edited copy into Checkpoint's folder, or (b) you didn't export the edited save from PKHeX, or (c) you didn't restore the save correctly with Checkpoint.
Here's a few things to try:
(i) After you pasted the edited save into Checkpoint's folder, try loading it in PKHeX to check if the edits are there.
If it's not, it means you did not paste an edited save into the folder (a).
(ii) After you export the edited save from PKHeX onto your desktop, close PKHeX, then launch a fresh window of PKHeX, and load the edited save into it, to check if the edits are indeed there.
If it's not, it means you did not export the edited save correctly from PKHeX (b)
(iii) If you confirm it's not (a) or (b), then it's likely (c). Try restoring saves from past backups [that happens to be on your SD card], then load the game.