Thanks Richard.
I took your advice and cloned the theme completely. There is not much advice online about how to do this, so I spent some time (using your guidence) and worked out the best way to do this. I have included a step by step guide below to help anyone else wanting to do this. To be honest, once you know how it is done it is very easy and takes approximately 10 to 15 minutes.
Instructions:
1. Grab a FTP programme (I used Filezilla) and copy your base theme folder from the 'theme' folder in moodle to your local drive and rename it to your new theme name on the local drive.
2. Grab a copy of CodeLite from codelite.org, Install and open it.
3. Click on the Workspace tab in CodeLite
4. Drag a copy of the theme folder that you have just copied into the workspace - you should now be able to see the full folder structure in CodeLite.
5. In CodeLite go to Search-> Find in Files -> Find in Files ... (you can press Ctrl - Shift - F)
6. In 'Find What' = adaptable (or your base theme name)
7. In 'Replace With' = adapt_new (or your new theme name)
8. In 'File Mask' select the option which includes .php .js .css (it includes many more too but this is OK)
9. In 'Look In' select <Entire Workspace>
10. Ensure 'Match case' is ticked
11. Ensure 'Match whole word' is unticked - (this ensures all variable names are changed)
12. Click on the 'Replace' button
13. Wait until the software has found all Matches (this only takes a few seconds)
14. In the 'Output View' click on the 'Replace Marked' button -
** Steps 5 to 14 replace all instances of your old theme name with the new theme name in all of the code structure.
15. Repeat steps 5 to 14 again but this time with capitalised search and replace strings e.g Adaptable and Adapt-new - this isn't essential, but helps you spot the new theme in the admin panel
16. Click on every folder in the workspace one by one and look for either folders or files named with the old theme name and rename them to the new theme name (I found files in 'jquery', 'lang/en', 'lang/es' and 'style' but this varies for each theme) e.g. "theme-adaptable.php" becomes "theme-adaptnew.php" - be sure that you get them all so click in all folders and subfolders.
17. Exit CodeLite (Save and Exit if asked)
18. Using your FTP programme copy the new theme folder back to your 'Theme' folder on your server
19. Once the move has completed Sign In to your moodle site as Admin
20. Click on 'Notifications' and finish installing the theme.
Once this is complete, you should now see your new theme in the Appearance -> Themes section of your Site Administration.
I hope this helps.
Mark.