Thanks for asking. I did reach out but no resolution was found. My best guess is that the problem was caused because I was using a beta version of Ulysses—the first time I’ve ever used a beta, and the last time I might add. 
I’m waffling on what to do about Ulysses. I like the app and based on the vast number of people using it for years with no issues, I’m not overly concerned about data loss. I just can’t decide if these two things make Ulysses worth it:
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The subscription. It is minimal for me because I qualify for an education discount. But, I’m still “renting” my writing tool, which means if I stop paying, I can’t use the tool.
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There is some friction using Ulysses when I export a document, I often have to clean up formatting after exporting to Pages. That represents friction. But, there is also the “overhead” or friction when writing in a word processor—larger files, dealing with the formatting, and what not.
I sometimes wonder if I’d been better off never having heard of markdown. I never once questioned using a word processor before hearing about markdown. 
Then again, there is this: