It is possible that you will lose something when you export to IDML, but it is not likely. It is usually safe.
After you open the IDML file once, then you can save as a normal INDD (indesign document) and it should be fast again.

Are those black dots real objects on the page? If not, then maybe something is corrupted in your document and you should try to export the document as IDML and then open the IDML file.

Blue dotted lines are often a signal that the object is on a master page, or that it’s a button, or that it’s part of a group.

Some of these kinds of equations may be very tricky. There may be some tips in these articles, though:
https://creativepro.com/auto-format-superscript-and-subscript-numbers-using-grep-styles.php
https://creativepro.com/quick-grep-to-superscript-ordinals.php

Sometimes you may need to use a tool like MathTools from movemen to create complex equations.

We’ve got a bunch of InCopy, XML, and automation experts coming to PePcon this year. Might be a good place to get some answers.