Nope. The CK doesn't track scripts like previous kits did since they're now external. You can recompile/check quest scripts, but that's it. If you go into your properties, in the script tab you can set a 4 character prefix that the CK will apply to all automatically created scripts, then you can manually apply this prefix to handmade scripts. The result being that all scripts are prefixed and you can tell what they are.
For example, if you entered the prefix 'KNEE' into the scripts tab of the preferences, it would make a script fragment for a dialogue info 'KNEE_TIF0104XYZ' instead of just 'TIF0104XYZ'. Same with package, scene, and quest scripts that the CK autogenerates. Then, when you make your own script (Like on a trigger, book, etc) just make sure to put the 'KNEE_'.
This is a wonderful proactive measure that prevents the kind of issue you're having, so while it wont fix your problem now, it will prevent it from ever happening in the future. (Unless another mod uses the same 4 characters, so make it unique, but even then it's unlikely) I figured this out about 4 months ago, and I spent about 15 hours tracking down all of Falskaar's scripts. Renaming, and then recompiling them. Now every single script that's part of Falskaar starts with 'FSKR_'. I know exactly how many there are, and where they are. This also makes it easier to pack up the source files if I wanted too.
Hopefully this is helpful. You have to manually track down all scripts in your mod, but start using this method to prevent this issue in the future.