Vita Save Manager 0.3, backup your saved game data. Detect cartridge for save dump. Download Vita Save Manager. I’ve always wished somebody would add a feature to homebrew like this to sync save files with Google Drive or the likes for backups and using on multiple devices.

3ds Homebrew Emulators
Save Manager
'You should be able to transfer the save using save_manager if you can run tubehax or the other hax's. Just backup the Sky3ds then restore to the eshop version. I assume it would be best to already have a save on the eShop to overwrite instead of just trying to create it from scratch.
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The homebrew, all credit goes to profi200 on IRC I was just at the right place at the right time to see the release. https://dl.dropboxusercontent.com/s/6vwld0sg4pkkvcp/save_manager.7z'
Found as a post on GBATemp. Seems to work