Hello, I learned how to “preserve formatting” when using other alphabet texts in the main body, but for some reason in the footnotes section, I cannot “preserve formatting” and I lose all of my alphabets during Compile. In the Compile, my settings are to font-override with Times New Roman because I’m writing a dissertation that has that font requirement. I need various alphabets (Greek, Georgian, Russian, etc.) to be preserved, however. Do you have any suggestions?
Try using Inline Footnotes, instead of Inspector Footnotes, for the ones that need special font treatment. I just ran a quick test and it appears to be working fine.
Yes, you’re right, with Inline Footnotes, I’m able to “preserve formatting” on foreign alphabets and they compile properly. I’m not used to footnotes appearing in the middle of my text… but if this is the only way to do it, I’ll do it! Thanks for the tip, and if you find any way to do this using regular footnotes, that would also be much appreciated.
Unfortunately there is only limited formatting control in the sidebar, which is why the Preserve Formatting feature doesn’t work there. Since you only need it for the footnotes with alternate alphabets, it will hopefully not be intrusive to have them in the text. I got used to how it all looks years ago (in part from having used LyX before, which had notes inline instead of hidden off in some box or floating in a margin), and came to prefer it for a number of reasons (never having to use a mouse to edit or create notes for example), so you never know. 8)
Oh my! A “document processor” I didn’t know!! 
Out of curiosity, I visited the Lyx website. I found it interesting until I looked at their OS X screenshot. It had pinstripes meaning it dates from OS X 10.2 Jaguar (if not Puma). At least 11 years old, probably older! But oh, how my studies could have been different if I’d known of it in 2002…
LyX doesn’t actually look all that bad on a modern Mac, they might just need to update that corner of the website it seems. It is cross-platform (same coding toolkit as Scrivener for Windows, as a matter of fact), so it won’t fit in perfectly, but there are no pinstripes! 
But yes, I used it for years prior to finding Ulysses, and as an interesting point of trivia, the inline annotation system in Scrivener 1.0 was inspired directly by LyX’s system, though not all of it could be implemented, such as the ability to hide notes.