So I have been doing some scripting recently. I edit the scripting files, and I thought that since I save my changes as an .esp file, my main Skyrim file would remain uneffected. That is NOT the case! The changes have effected my main file. Why is this so, and how can I change and fix this?

Delete the scripts, and then have steam verify game files?

This happens because Skyrim doesn't store scripts in .esp/.esm files.

So how can I prevent script modifications from effecting my original game? Sometimes I must edit scripts to make a something work, but I don't always want the effect to be permanent....

New scripting system unfortunately comes with this caveat.

The recommendation is to ONLY make new scripts, never to modify existing ones.
I have found that when you stick a modified existing one into a bsa, it doesn't even work.

If you're modifying a quest script, you can "rename" the script to turn it into a new one.
("Quest Stages" Tab, "Advanced" tab near the fragment, "Rename Script" button)

EDIT:
You can make a backup of the source code file you want to change, then restore. If yo ustuff up anywhere, getting steam to "Validate Tool Cache Files" will redownload any scripts you have modified.

Also, changes to the source code files will not affect your game, the changes will only take effect if you compile the script. Removing the compiled script file (*.pex) will remove its effects, though if you want to modify the script later for a different mod you'd want to have the original source file again.

See this post:

http://www.gamesas.com/topic/1344036-warning-about-the-new-way-scripts-work

Create new scripts?