Can you please be more specific & provide details.
We can presume that the "3" or "5" audio passthrough options you have available are within Kodi, and/or that it's the two HD audio passthrough options that seem to keep disappearing. However, without you providing any additional details there's really very little anyone can comment on with any certainty as yet.
Which firmware are you running on your U9-H, which multimedia software & version are you using, what's your external hardware, & what steps have you taken so far to try to resolve the problems? (All would be a useful start.)