Ian,

I have a suggestion that may help you avoid a future problem - create a semi-blank template with only your common content (NavBar, styles, named colours etc.). This will avoid redundant PDFs being saved across from one branch XAR doc to a new branch XAR doc.

1. Save one of your branch docs as (say) 'branchmaster.xar'. As I expect you are doing already, delete any content you do not want to retain (in this master) and Export the doc to a NEW directory.

2. From Windows Explorer, in the directory you exported 'branchmaster' to, delete the two folders, 'index_htm_files' and 'branch master_xar_files' and Re-Export your 'branchmaster.xar to the same directory. This removes everything and creates a new start point / master doc. Save this doc either as a standard XAR, or use 'save template'. Now, when you start a new branch, save it under a DIFFERENT NAME - BEFORE you add any content. Only PDFs pertinent to that particular branch will be saved.

BTW: I can replicate the issue you describe, that is for example take a couple of images, link them to PDFs save and export. Delete the images (and links), export again and you will still see the PDFs in index_htm-files. I think I understand the logic, but it would be better explained by @Acorn.