Script Closed/Out of Range
If you are working on a script in the editor (with open files, that you don't want to lose) and your in-world script is closed, or goes out of range, you will temporarily lose contact with the second life version of the script.
To restore contact, you will need to re-open the script in second life to be able to edit it again. After clicking "edit" it will load up another instance of the editor. (Clicking "Edit" restores the contact, and you will probably have 2 copies of the script and editor loaded.) The script NAME that you are working on should be the same NAME as the one in the FIRST editor instance. Assuming it matches, you may safely close the SECOND instance of the editor, and continue working on the first.
Alternate - when the script opens the first time in the editor with the SL filename, open up any included files, and save as a project. When it loses touch, open the script again in SL, click "Edit" to restore contact, then open the project.
To test any of these, just save the script, and it should update in second life as usual.
Alternate/Zero Effort: Close the first editor instance that lost contact, and just edit it in the second instance.
Does not load from Second Life
If the editor is not loading from Second Life scripts when you click edit, open the options window from the main menu, tools/options/ and make sure "Set Environment for Second Life Script Editor" is ticked.
If you are using a third party viewer that is not based on the viewer2+ codebase or does not use environment variables, it may be more complex (Hello Phoenix)
If you have updated the editor(or environment options) while running Second Life, you may need to restart Second Life for changes to take place (sorry).
Unable to check for update
Due to the Microsoft Click Once installer(and version system) used, it is not currently possible to check for updates when the editor is loaded from Second Life. Running the editor from the start menu, or by double clicking on an .lsl file on your hard disk should allow updates to occur normally.
Issues
There are a few minor issues with the preprocessor not working 100% as expected, usually due to migrating from another preprocessor. Most problems can easily be corrected by a few minor formatting changes in the original source - it is suggested you check the master file for any errors in the preprocessed code.
Currently you may only have one master/work pair open in each instance of the editor (but as many normal code files as you like)
..a blank line is currently needed at the end of the file, and the preprocessor does not highlight the last line.
Workaround: Add a blank line at the end of the file.
..saving a blank file currently behaves unexpectedly
Workaround: Save as, then reload the file.