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I admit it might be confusing and adding to that some session renaming was buggy but, as you also know, it's been addressed recently on your request :)

there are probably two issues here, that also add to confusion:
a. changing the session directory;
b. changing the session name;

while a. affects only new files that are to be recorded and/or created thereafter, b. changes all existing files in their names--it was the later that has been marked buggy and leading to empty clips, especially if the clip has been copied around the timeline (linked). this is what has been fixed.

anyway, the best and highly recommended method to backup and relocate sessions (or projects if you prefer) across the file-system or even machines, is the archive/zip bundle method (*.qtz). do please do not try to move any files and/or directories around: that's really crazy and you should know that, if you've been doing that, you're doing it on your own risk.

one other thing that probably relates to some reported problems with said sessions used as "templates": qtractor has a special file suffix or extention to denote session templates: .qtt; you're advised to not use regular session files (*.qtr) as "templates", especially because they will retain the session name and directory, that you, most probably, will change it to whatever; always try to save as a "real" template file (*.qtt).

hth.
cheers

ps. as always, not dismissing on anyhthing, surely there's lot of thing on this regard (and others) may well be improved, but currently, it's all what there is :)