Replacing with <empty> does not work with history
On Mousepad 0.5.9, with non-empty strings on your replace history, if you try to replace some search string with `` (empty), then the first option is automatically selected and is used as the replacement string instead.
So those looking to delete that search string must either clear their replace history*, or disable it entirely.
*doing this with dconf Editor requires restarting Mousepad for changes to take effect. See /org/xfce/mousepad/state/search/
.