When doing your second epub to epub conversion what do you have in the Convert - StructureDetection - Detect Chapters at
I try to avoid epub to epub conversions just in case I get the TOC messed up. If I do have to do one I set the above box to a single forward slash, /
- I also set all the TOC boxes on the Convert - TOC
page to blank. I don't know whether this is guaranteed to work but you could give it a try.
Edit: Oh and make sure Convert - TOC - Force use of auto-generated TOC is unchecked.
Looking at a couple of different approaches to your cover problem:
- If your pre-conversion epub was also created by calibre then merely re-sending the epub to the reader may update the cover as part of the send. Whether it works depends on how the cover is defined inside the epub, but calibre does its best to make sure the cover is the current calibre one.
- I don't think you mentioned which reader you have but if it's a Sony PRS-x50 there are ways to make sure the cover thumbnails on the reader match the current calibre versions. It may not matter as much to you what the cover looks like on page 1 of the epub if your Sony bookshelf cover thumbnail is correct.