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Hello,
I may not comment on whether turning on Kobo with empty SD slot will erase previously present annotations. But if you happen to use KOReader and if you'd like to try to recover annotations etc. through recovering BOOK.epub.lua file within the associated BOOK.sdr folder, you can try cgsecurity’s PhotoRec. Just start the program, chose SD disk, 'scan free space' and choose 'txt' file as the type of files you want to recover.
Look through the bunch of recovered text files with incrementally increased file size and check if they contain book titles.
I use lftp to mirror my books folder on Kobo SD card and the other day I forgot to put -R switch so the upload and download operations were messed up, which resulted in the exact same situation you mentioned, all latest annotations were gone. But I managed to recover the *.lua book info files by the method above.
Good luck!
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