So, I have an old powersaves backup for alpha sapphire that I'm trying to restore to a digital version using checkpoints. However i can't figure out how to get checkpoints to recognize the .bin file. Any assistance would be greatly appreciated.

its basically as you say. powersaves are a different save file system. They need to restore and decrypt it. and load it over.Never had a Powersaves. My guess is that those saves are stored in some proprietary format, possibly encrypted. Commercial products tend to do such things…
Try:
=====
- Restore the save in question with Powersaves into the cartridge it came from
- Backup the cartridge save with Checkpoint
- And finally restore this decrypted backup to the digital version
Well prepared for some "I don't have […]"-reply:
Maybe somebody else knows more about this hardware and can tell you a direct way.
It probably didn't work for you right? Have you managed to make it work?I'll give it a try with a new cart. (original cart was stolen.)
Thank you.