When exporting to epub, a table of contents with the ‘scene’ titles is automatically generated. Is there a way to get rid of this, or change the chapters to numbers? I think I managed to do the latter once, but I can’t find the setting.
Thank you in advance 
Go to Compile>Formatting and mark the checkboxes that you want for each Level. You will want to unmark the ‘Title’ checkbox for scenes. If you click on a row to highlight it, the level of that row is also highlighted in the Binder. For Chapters, select that row (usually the top level folders) so you can click on the Section Layout popup in the Compile>Formatting window and enter a Placeholder Tag (See that section in the Appendices of the Manual) for example; Chapter <$n> in the Prefix box will increment by one each time it is encountered and add it to the top of the section. You can see the result of the setting in the preview window at the bottom of the Compile>Formatting window.
I see, thank you, I had that entirely deleted, because I didn’t want Chapter N showing up in the text 
Right now, the only box I have checked under Formatting is ‘text’ for Level 1+ and nothing else. Am I doing something wrong there?
The top levels are all called Level 1+ which one are you talking about?
Level 1+ with the blue folder icon: This is usually the chapters - all boxes unchecked because you added the prefix Chapter <$n>
Level 1+ with double page icon: This is used only if you have text pages nested within a text page
Level `+ with single page icon: This is usually where each scene is - text box checked
Sorry, all boxes for the folder level are unchecked, and all boxes for the two page level are unchecked, and only the box for the single page level for "text"is checked, with all boxes unchecked. If I leave the text/text separator as empty line instead of page break, there’s no issue.
I see what you mean, it does that to me too when using a page break between text/text documents. I have mine set up so I’m using the custom setting to insert a row of characters, most people use ### or similar, so I’ve never used it your way.
Dunno, this is beyond me. You could make a small test manuscript and test some of the settings and file/folder nesting. Maybe this is where that nested text within a text thing comes into play? So maybe that would be the row with the double text pages Level 1+.