I guess your issue is caused by the two stage save feature (described below), disable it and see if it still happens.
To prevent data loss in the unlikely case that jEdit should crash in
the middle of saving a file, files are first saved to a temporary file
named #filename#save#. If this operation is successful, the original
file is replaced with the temporary file.
However, in some situations, this behavior is undesirable. For
example, on Unix this creates a new i-node so while jEdit retains file
permissions, the owner and group of the file are reset, and if it is a
hard link the link is broken. The “two-stage save” feature can be
disabled in the General pane of the Utilities>Global Options dialog
box; see the section called “The General Pane”.