Make a table to document the Markdown characters that get converted to something else in the compiled manuscript.
For example,
| Markdown |
Manuscript |
Reasoning |
--- |
Centered # |
Traditional scene breaks are hard to replicate in Markdown. Use a horizontal breaks between scenes in a single Markdown document and convert them to a centered # |
There’s probably more examples of conversions (now or in the future) so get them documented now.