I had a mildly annoying experience with the NetBeans IDE recently, and I'm making a note to myself here what to do if it happens again.
I was debugging a Java program that I wrote using an open-source library, and it became necessary for me to set a breakpoint in the library code. This was a first time experience for me: I use open-source libraries extensively, but I virtually never open the source code, and in fact I usually don't bother to include the path to the source code when I define the library in NetBeans. I've found that nothing spoils the taste of the sausage quite like seeing how it was made. :-)
At any rate, when I opened the source file to insert the breakpoint, NetBeans warned me that the source file "cannot be safely opened with encoding UTF-8" and asked if I wanted to open it anyway. I said yes, it opened, I set the breakpoint, found the bug (in my code), closed the source file and that was that. Or so I thought. There's a discussion of this warning on the NetBeans support forum, including various possible remedies (including converting the source library to UTF-8). That wasn't necessary or worth the effort in my case, since I was opening one file, one time only.
The first occurrence of the UTF-8 warning wasn't bothersome. What was annoying was that every time thereafter that I opened the project in NetBeans, I got the warning. Whether I answered the "really do it?" question yes or no did not matter; none of the source files opened, and the IDE thereafter gave me no grief ... until the next time I went into that project.
It turns out that I had left the breakpoint in the source file set. Even though the source file was closed, and I was not attempting to reopen it, the presence of the breakpoint was apparently causing NetBeans to look at the file, see the non-UTF-8 encoding, and nag me. Once I figured that out, the solution was simple: remove the breakpoint. Note to self: be extra careful to remove breakpoints from foreign source code in the future.