Custom post types meta fields problem

I have created a custom post type with additional fields (books, for a web site for a children’s author) and it all works well: creates, edits, deletes etc.

However, I’m now playing around with adding more functionality (taxonomies, new types etc), and every time I re-upload my functions.php file all the extra data in the postmeta table for my custom type gets wiped out.

I’ve tested it pretty well and I’m sure the new functions.php is triggering the issue. Apart from being annoying while developing, I can see this being an issue in future if we ever want to make any modifications to the site once it’s fully populated with data.

Is this intended functionality, a known issue, or is there something wrong with the way I’m writing the code? If I were to create my custom types a different way (as a plugin perhaps?) would I avoid this problem?

Any advice greatly appreciated 🙂