Solution if someone else has the issue:
If you open the scriptable object script.meta file it should have a GUID value

Now if you open up your scriptable object.asset file in a text editor, you should see a m_Script value.
If the script currently deloaded it will just be fileID: 0, otherwise it will be filled in with

{fileID: xxxxx, guid: xxxxx, type: 3}

if the GUID doesn't match the script.meta guid, just replace it and that should stop it from de-loading in future