Clearly Notepad++ is long out of beta - unless you used a test version of some sort. While no software is completely bug free, my guess is that there is something else going on here.
How big was your file - I am wondering if the save operation took an appreciable amount of time, and there was some sort of unfortunate interaction between NP++ and Filexilla.
You really should use a backup system of some sort - but for now, possibly the hosting service for your website has backups that you could access.
You might find something in:
%AppData%/Notepad++/backup
To resolve this problem, you clearly should experiment with a copy of your file. If you can reproduce the crash, you should disable any plugins and see if NP++ crashes.
The strange thing to me is that NP++ clearly hadn’t crashed at the point when you saved your changes and went back to Filezilla - so why did it crash while you were using Filezilla?
Did the crash message say anything useful?
David