not up to speed on wysiwyg apps like this but...a real quick way to lose any formatting for text files I know of is to save it in a traditional unix/bsd format and have it then read on something that speaks "windows" text format.
There are better terms for this text formatting that a bad Monday at work is having me forget but when I save to .txt I know to make it more universal I save in an encoding windows can read. Otherwise a say windows system will get a rather ugly text file with most encoding ignored.
Your app is not looking like a mac only app so internally it may not be reading unix/bsd txt encoding (carriage return coding can vary between .txt standards for example).
Beyond that I am not sure if wysiwyg's are keen to raw imports and prefer you write in their editor. I do know I have used a few markdown (.md) editors where if I factor in repair time to the mess a copy/pastes makes...I am usually better off rewriting from scratch in the .md editor. At this point...any .md work I do (readme for my github stuff a common use) I now do from scratch in a .md editor to avoid this headache.