I have attempted to upgrade Opencart 1.4.8 with custom theme using update script but it deleted the custom theme as it was actually set as default theme. How can I prevent this from happening so I can use this same theme for new version 1.5.1.2?
Also will this custom theme be compatible with 1.5.1.2 version?
No, it wont. The only way to stop it is to create a custom theme and set it to that. You don’t need to copy all files over, but a few usually like header.tpl, footer.tpl and a stylesheet, then if you make any customisations, either use vQmod or create that tpl file in your theme folder, and copy the content over, then edit