I'm running into the same thing. MacOS 10.13.6 with latest version of Evernote. I'm not noticing the missing lines on regular paragraph separation, but I am noticing it on everything that I indent. For example, I have a note where I am outlining Sunday School material. Regular paragraphs double-return fine--they keep the separation. When I am adding scripture references within the note, I will indent and italicize the Bible and Book of Mormon references. If there is more than one verse, I double-return between the verses. This is what disappears for me after I close the note/app and return to the note.
I pray (literally) that whatever changed recently can be fixed quick. I have hundreds of quotes that were affected, spread out over various notes and notebooks. Not sure what happened or when, but I only noticed this recently.
