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ok, i've been testing this a little further...

funny thing so far is that these midi clips only get lost if they are created on a brand new and empty NSM session... if you add the tracks, save, close and re-open the NSM session, even though the tracks are empty, the issue with any new clips missing later does not seem to happen anymore.

and it is not exclusive to midi, recorded audio files are missed too; however the files are not lost they are only linked in the qtractor session file (.qtr) by their sym-linked names that are (wrongly) stored in a different location, outside of the NSM session folder.

suspicion goes that this bug was lurking in there since v0.9.0, almost one year ago... yes, confirmed: the previous release v0.8.6 works fine in this regard.

seeya.

[UPDATE:] Maybe fixed on qtractor-0.9.4.1git.b9c293. thanks.