Compiling: Replace in Footnotes


I am writing in Scrivener, with a little bit of MMD to produce a LaTeX document. I am putting in some LaTeX code directly, and I want to make some global replacements in the compiling process to turn them into correct latex code. However, while this works fine with text, it does not with inline-footnotes. The replace command seems to only affect the text, not the inline-foodnotes.

What can I do?