ps - there is a long thread here, which explains why covers are not updated wiithout the 2nd conversion
https://www.mobileread.com/forums/sho...=covers+kindle
short version: cover is not considered to be part of metadata ( even though you confusingly have to edit it on the metadata screen)
so your issue becomes one of why am I losing chapter navigation.
how about this time turning on the bells n whistles - turn on the heuristics - detect n markup chapter... option & see if that helps.
I convert into epub & use epub tools to get everytign as it should be, then convert back to mobi, that way I can examine the code, & epub code is easier to understand + is more accessible.