Hi Eddie,
All the changes that you've mentioned - slurs, font, etc - will only be held in the .not filetype. The .mid (MIDI) filetype does not keep that type of printout/look information - it only keeps the actual performance information (eg. note pitches, durations, instruments, etc.)
Please note that if you open a .mid file in any of our products and then save that file (rather than use File/Export), there will then be (1) the original .mid file (unedited) and (2) the edited .not version (which is the default filetype that our products save).
My guess is that you did all your editing, saved the .not file, but opened the .mid in Notation Player. Please take a look for the .not version of the file and open that in Notation Player - I'll bet all your nice slurs and font changes will still be there
(side note: slurs are different from ties; ties will show up automatically, but slurs are an added "annotation" only present in the .not version of a file.)
ttfn,
Sherry