I have made a HDA for my project to work inside of unreal. Just realised it would not connect with an apprentice lisence.

Now if i get an Indie license will the hdanc be converted to hda automatically when i save the asset?

If you open an NC file in Indie the session will be downgraded to an Apprentice session and can no longer save in Indie (LC) format until you restart Houdini.

Sidefx explicitly offers a one-time conversion of NC/LC files to full commercial when purchasing a license (files have to be sent to Sidefx), but a quick google doesn't turn up an equivalent for NC to LC.

You should email sidefx support for a definitive answer.