If I understand your question, you're not having issues with implementing the type-ahead, but maintaining the functionality after a manual edit in the metadata schema WYSIWYG editor.
If that's the case, then that's a tradeoff we've encountered and decided to live with.
The revision of custom metadata types is something we've also observed and seems to apply whenever you make customization to OTB metadata.
The options we've considered are as follows:
- Never customize metadata to maintain the WYSIWYG editor functionality.
- Always deploy metadata via code in order to allow and maintain customization.
- Greatly increase the complexity of our metadata customization efforts to also customize the metadata WYSIWYG editor whenever we make an edit.
Option #2 has seemed the right balance. Metadata structures don't change so often and business users aren't so enamored of making these changes themselves that option #1 adds a great deal of value. We've never spent a ton of time digging into #3 to determine if it's possible, but the argument against the benefits of the WYSIWYG editor also argue against this investment.
Hope this helps,
Beau