Calibre not using my indent command

[JSWolf]

Originally Posted by Karellen

Oh, right. You are trying to make all these edits using these rules in conversion dialogue.
Don't do that.

Open your epub in the Editor and make your edits there. Teach yourself how epub coding works, rather than that hit-n-miss approach in conversion. If you don't, you are always going to run into problems and unable to figure out why.
Even your comment "I don't have a stylesheet" is a major red flag issue. Of course you do, but you don't know what it is or where it is. So how can you possibly fix any coding issues?
So, go ahead, open the epub in the Editor and look at how an epub is built.

@ryder, I agree with this. You can't just delete the CSS and hope your CSS will fit in and work as you want. That's not happening. You have to see how the ePub is made and then you have to make your changes so they work. So you have to see the internals of the ePub and go from there.

The more ePub you edit, the more you'll understand what's going on. And it can very wildly.