I use Notepad++ with both English and Hebrew. As a result, I frequently have to change the direction of the text (ctrl+alt+'R'/'L'). However, when I do any of that, it reverses the whole document, including even the line numbers. Strangely so, if I minimize the window and open it again, it gets fixed.
Any reason for this peculiar bug? Any way to fix it?
Yes, it is seems to be a N++ bug in v6.5.
There are related bugs still open, see #1721, #3781 and I don't know if this is a coincidence, but a few hours ago the exact same bug that you found has just been reported, see: #4550!
As a general comment, if your language is a right-to-left one (like Hebrew), I would suggest to try another editor in complement. Because at some point you will need to edit a bidirectional text, and Notepad++ is not good handling that (has limited support). Check this Wikipedia list of text editors supporting RTL & bidirectional (and notice N++'s entry).
Old Notepad++ versions work OK with this function...
Search for Notepad++ Pro.v6.3.3.rar that also include user.manual guide not present in recently versions.