Right now, I know of two choices (with 0.25.0), I can either save ALL par2 entries, or none if I reboot my PC or otherwise restart Alt.Binz. Neither is perfect, in fact what would be nice would be to save par2 entries until they unrar successfully, and then delete them.
Also, it would be nice to set the download list to clear when the download is done, or after some customizable number of days from completion.
Have I missed a setting or is the above a feature request? Those might be worth donating towards/for.