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The audio files must be located in the vary same path and directory names where they were recorded or imported into the Qtractor session. You said you installed a fresh system, so it might be a change some directory path name have changed or simply does not exist in the new system.

Open up the session file (.qtr) on a text file editor and check all the filenames. You can either move the missing files to the older location or rename all the missing or non existing paths in the .qtr file.

Cheers