Actually running older versions of LW will cause issues with the download.dat file. Though going back to the new version and forcing them back via the Library window > incompletes will get them back to the download window & though initially show zero %, once start downloading will show their previous download %.

It sounds like the torrent site binding to a specific version of LW is an issue.
Is there anyway to change that?

AFAIK regular programs should not be used in safe boot mode under normal circumstances. I have not attempted to do what you are doing.

BTW if you are still having problems with download.bak, there was a backup system posted before LW introduced an improved download.bak management system (my guess is based on the one that was posted or at least their own approach to the issue). Check the OSX section stickies on the forum to locate it.

Mac makes their own Java unfortunately. It has never been as good as the Java for other OSs. It has always tended to have memory leaks, and difficulty releasing VM when no longer needed. Keeping in mind LW is mostly made from a type of java and runs on java.

When running LW with either or both large shares and incompletes, VM (Virtual Memory) will run up fast, and LW will after a period of running get slow and potentially get close to crash status easily .... losing responsiveness. Simple answers are: to close LW periodically; reduce incompletes, Tip: Purge the Downloads Queue! (click on blue link); keep shares below 2,000; not share from slow external drives such as FW400 or usb.

As far as keeping old incomplete files, they are useless unless you have a healthy download.dat/bak file that recognises them. Else LW will just ignore them or think of them as an empty incomplete file. Not sure if hash info will be stored either, which means the file(s) identity and source may have been lossed. Stief will probably know more.