According to this post as well as several others that I have read, this is not a feature and cannot be achieved as of now.
Notepad++
-Only allows you to mark the words for the time being.
-If notepad++ was to save the files with highlight format only Notepad++ would be able to use the files made. Unless the user deleted all highlighting before trying to use the file.
-Looks like this feature has been wanted for a while but no plug-ins have been made that I can find.
The Above answers your question on Highlighted text not staying after a restart.
Because in Conclusion the Program is not made to save the Highlighted Text it is only a visual for the user when you are currently working on the file.
The Highlighting is also setup for use as Replacing highlighted areas with text as example is stated here Notepad++ - Highlight text and insert html Hope this helps.
Sublime May offer some plug-ins that the User will have to configure.
There are several add-ons available one option would be this one would be this How To Set Up Sublime Text for Markdown Editing
Only issue with sublime is it costs and at the time is set at 70$ a license
1
This post here should help you out. http://superuser.com/questions/567703/permanently-highlight-all-occurrences-of-text-in-notepad
– NetworkKingPin – 2016-04-15T06:57:06.847Thank you for the reply but it doesn't cover my problem. They are all gone after restarting the notepad++ instance. – takobaba – 2016-04-15T06:58:22.467
1You are right I just tried it. Im going to look into this. – NetworkKingPin – 2016-04-15T07:16:10.167