I tend to keep large numbers of files open in jEdit at the same time. Currently 36. I work on some files for a year or more. I usually search a few of these files backwards. Thats alt+b each time, then alt-o to switch back to forwards search. As best I can tell 4.3pre16 has no way to set search options by buffer.
You can insert the Buffer-Local Properties :folding command into a buffer to persist folding. How about something like :search=backward to default the search direction in this buffer to backward. Perhaps other users have additional search options that they are constantly setting for certain files that this could persist as well.
I suppose Utilities > Buffer Options could also support this, although I am able to mark up my files and would prefer to set search options in the file.
The search dialog search direction could then change automatically when changing buffers. If you manually override the Buffer-Local Properties then jEdit should remember the over ride as you switch buffers, until you reload the file, as it does for folding.