If you get an error message that a script is not responding, asking you to wait or stop, click stop. You can continue your edit, and it won't affect what you're doing.
If you erase the data in an older chapter (just leave a sentence), click edit chapter, then go back in, REMOVE that line or word, and copy/paste the chapter data back in.
If you're using Word, you MUST use the "paste from Word" box. Also, don't try and add this from previously exported files from Word, that are now html files. Go BACK to your original Word doc. Word, when exporting to html, unless you filter how it does it, adds roughly 4 times the chapter data in extra code that isn't needed. This is what makes all the extra line spacing, is Word itself, after it's exported to html format.
When you initially added the chapter, what did you do, to do this?