You’ve already seen why this is not going to work the way you want it to. There are ways using Text Suite and the text property of paragraphs, but that’s a PITA. RTF is a pure text format on the surface, but in fact it uses formatting interspersed with text. Changing the underlying text by changing plain text probably messes up the whole structure since RTF is no plain text in the classical sense. There’s already been a similar discussion here
Use Markdown for that, nowadays it even has boxes that can be used for to-dos. That is a real text format, i.e. the mark up is very limited, very simple and very easy to parse. And replacing text in the plain text of a MD file does not break anything, since formatting is done externally, via CSS.