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When you open a file, then you open the file for editing, when you import a file you only use the content of the file not the file it self.
The proper action as I see it would be to create new midi file(s) for the content of the imported track(s).
i think i understand your question now. let's put it this way. qtractor works as designed by dealing with midi files as its external storage midi data format. ie. midi data are always stored and retrieved from standard midi files (smf).

now please note that a qtractor "session" is a collection of references to all the midi or audio files that happen to be in use. those files, or better yet, references to those files, have been eventually "imported" into session by user request. nb. file drag-and-drop is fundamentally the very same operation as "importing" the same files. you just put files, or parts of them (clips) into tracks under some sequence, thus the moniker "audio/midi sequencer" ;). no more, no less. in qtractor there's no distinction between "importing" or "opening" a file. got that?

also, qtractor session files do just refer to media data files (audio or midi), something that some other programs may call as "links". qtractor always refers to media data as external "links". it doesn't copy any files around the file system into some session directory. the file stays put where it is originally located on the file-system. the session refers (links) to the files, simple as that. ok, calling it "import" may be kind of a misnomer but see that's called "importing tracks" (in abstract sense), not quite exactly "importing files" (in concrete sense) ;)

now you ask: you changed the midi data on the midi clip editor, for instance and now you want to know where the new or modified data will get saved/stored. you may now guess it right that the new and/or modified contents is saved/stored into a genuine standard midi file (smf), either the one previously referred to or, most likely, a brand new one (often with some revision numbering scheme added to the respective file name).

maybe by this time you're a lot more confused than before :)

hth.
cheers