Hello
I'm runing Mate desktop under Mageia Linux
[eric@localhost ~]$ uname -a
Linux localhost 4.1.15-desktop-2.mga5 #1 SMP Wed Jan 20 17:05:51 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
I'have several script, xxxx.sh who are executable, if i edit them with Scite and save it, they loose exec permission, if i use another editor, they keep it
Works for me with SciTE 3.6.5 on Ubuntu 16.04, retaining the 'x' flag. Perhaps you, or your distribution, have turned on save.deletes.first=1.