About a year ago, I was having similar issues with an Amazon Pendant. During my research at the time, I noted a number of complaints about audio sync issues regarding user added video apps on later Amazon devices (4K Stick, Pendants and Cubes).
With my device, if pass-through was enabled, the audio went progressively out of sync from the beginning of playback. If, I stopped, and then again resumed play. The audio was again fine until the sync again became intolerable.
If I forced Kodi to re-encode the audio, the sync was fine throughout the duration of playback. What I discovered was that this has nothing to do with Kodi and everything to do with Amazons modified Fire OS.
Read here.
Apparently, at least the way I understand it anyway. They chose to use ExoPlayer instead of Android Media Player in the OS, and this is where the audio sync issue arises.
Long story short. I decided there was no programing Amazon offered that I could not live without and shelved my Amazon devices and bought a Beelink box and haven't looked back since.
As a matter of fact, I have been so happy with the Beelink box, I just ordered 2 of their S905X3 boxes. And the developers of CoreElec have already got it running on them in the nightlies.
Amazon devices, in my opinion, are just a pain in the ass.