Yuo have to make sure that you do never mix users!
Running JDownloader once with root requires you to start it ALWAYS with root unless you fix ownership again.
I guess you started it once with root and that's why JDownloader no longer can read/write the lists and fallbacks to importing older ones. As JDownloader uses CopyOnWrite for storage it is nearly impossible to loose all 5 (default) backups of linklist.
Please make sure to fix ownership
sudo chown -R user:group /usr/local/jd/
replace user and group
Lists are never deleted but backuped to .backup file. You can simply remove the .backup and increase number of file to be the highest one. Then JDownloader will read it on next startup
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JD-Dev & Server-Admin
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