(1) After updating from X9, EndNote had two libraries (one old and one converted). Nevertheless, every time I opened EndNote 20.1 it would ask me whether I wanted to convert my library. This continued until I set the preference to use the converted library by default.
(2) At one point working through the above process, I asked EndNote 20.1 to convert my library and save it back with the same name. EndNote let me do this! It overwrote the library it was trying to convert from and crashed. Then there was an empty file as the library. Thankfully I had a backup.
(3) At another point during the process I changed the name of the library.enl file. Then EndNote 20.1 asked me whether I really wanted to use a library without an associated data folder. This was confusing until I realized that the data folder needs to be named the same as the library, so I needed to rename both the file and folder. Perhaps it could have asked me to point to the data folder instead.
(4) EndNote 20.1 still displays PDF files (in the small viewer) starting at the bottom of the file rather than the top, the same behavior as X9. This is annoying because I always have to scroll back to the top of the pdf file in the viewer. Please change this default.
(5) Command+F is not a shortcut for find when in the large pdf viewer. Also, the only way I see to go to the next instance is to press the arrow after finding (rather than Command+G or enter). This makes the find interface somewhat slow to use.