I've made a mod which alters the way the game sends the player to jail. I start the 'quest' by changing the existing scripts for guard dialogue when the player is arrested, removing the existing code which teleports the player to jail and adding my own code.

The problem is this seems to permanently overwrites the script for the guard dialogue so that if you uninstall the mod getting arrested is broken unless you have the backup of the original script to overwrite my modified version.

Is there a practice I should be following to avoid this? I can't think of any other way to get my mod to work without altering the arrest event guard dialogue.

Maybe if you convert the scripts to a bsa file they won't overwrite the original scripts. Maybe this will work.

When I tried creating the bsa the CK did not give me the option to include the original scripts I had modified, only new additional scripts I had created.

Look at this tutorial maybe you will find something useful http://tesmods.blogspot.com/2012/02/adding-images-to-skyrim-books.html

One option is to rename your modified script to something else, and then replace the original referencea with your modified script. This increases the liklihood of conflict as you are now also modifying the containing quest that points to that script, but this shouldn't be too much of a problem.

Rein, I'm not sure that's the link you intended, but a quick internet search has yielded fortuitous results on how to change the content of bsa's. So if I include a script with the same name as a vanilla script in the bsa, my script will take priority if the mod is active?

Elseagoat, if I understand you I'd still be modifying the vanilla game, just earlier on in the chain, so I'm not sure how that would make a difference. Additionally, the script dialogue I have modified is started by an event, so I'd have to remove it from the events completely if I was to have one with a different name.

Just don't include the source file to your scripts and problem solved. Vanilla scripts are stored in a BSA, you won't override them (this is not true for the source codes). So, once someone uninstall your mod, deleting your script is enough to have the game running as before the installation.