After I found out about this little bug here, I decided to write a HTML/Javascript tool that checks JSON files for duplicate entries.
To use for C:DDA: Type ‘id’ into the text box and uncheck the check box. Click the Browse button and select any C:DDA JSON files you want to scan (selecting multiple files is OK). If any file contains the same ID more than once, a warning listing every duplicate will appear under its name.
Please use this before submitting a particularly big change to the JSONs!