I don't know about the problem, it may have been just a rare problem (BWT you do NOT need to select, it operate on the entire file but you need to save after the conversion).

Once the EOL are fixed if you use only a good text editor it should preserve EOL as they are and it should NOT create empty lines in the first place.
Notepad++ always preserve EOL as they are, it will change them only if you request it.

An AS forum recommended I use TextWrangler instead of TextEdit because it will not suffer the same problems & has far better applescript support & can run scripts directly (I'm guessing in similar way to how Notepad++ might be able to run script or program code.)

The other text program I started using occasionally from last year is called Sublime Text 2. It's advantages are that it preserves formatting & preserves MacOSX permissions of the file. But I normally use this for editing code (with exception of putting the host-file in reverse order. ie: some gnutella apps read the host-file from bottom-up due to the way it's loaded.) Edit: I have confirmed Sublime Text 2 is maintaining the original EOL.

Whilst using Notepad++, I again ran into issues with both the large hostiles but this time it was limited to the last two lines. Always the last array on last listing had lost a number or more. In the image example, 4 individual numbers are missing on the last line which includes the entire last array. This might be Win 8 related. I normally do my Win text work on XP after finding an anomaly with text handling either on Win 7 or 8 a few years ago.



I've released v.4 update.

Again, many thanks for your help.