When I have symlinked directories containing logfiles, and this symlink changes, when presented with the "reload modified files" dialog and selecting "Close", the files are not closing. Here is how to reproduce this scenario:
1) Create 2 directories under the same parent: "prev1", "prev2"
2) Create 2 logfiles: prev1/a.log and prev2/a.log. Make sure the contents of these logfiles are different.
3) at linux prompt, "cd" to the parent directory of prev1 and prev2
4) In this parent directory, do "ln -s prev1 curr", which makes "curr" point to "prev1"
5) Close all files in SE
6) Open "curr/a.log" in SE (important to use "curr" directory as this is the symlink)
7) At linux prompt in another window, change the symlink for "curr" to prev2 by doing: "rm curr;ln -s prev2 curr"
SE will say that a.log has been modified, at this dialog select "Close" for a.log
9) Notice that a.log does not get closed
This is a real scenario that I encounter all the time - it is not contrived.
Each time I do a new test run, a new directory with a timestamp is created (analogous to the prev1 and prev2) and many logfiles from my test run are placed there. "curr" is symlinked to the latest test run directory. This makes it easier for me to find the latest logfiles.
I have also noticed some other issues where in the "Files" tab I select one of these logs and press "DEL" key to close this file, but instead a different file is getting closed. Have not yet found a 100% reproducible way to recreate this, but maybe when you analyze the first scenario you could see how this 2nd scenario can occur.