OK folks, here is what I’ve done to resolve this issue. If anyones see a problem with this please let me know ASAP so that I can adjust things before we do the next release.
I have changed the code that breaks a file into lines when loading files to always return the default line ending for the last loaded line. Thus whenever a line is inserted after it the line ending characters will be there in the file when it is saved. The "CR/LF at EOF" option still determines whether the last line is terminated with line ending characters or not.