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Just pushed fix for crash to master. I will not add the capability to replace single or multiple existing html files at once due to issues with renaming when not an exact match but only a match due to case insensitive filesystems. Renaming even one of a set will/can break links to other html files, toc, etc, etc,
So the solution to wanting anything else is to:
1. keep a template epub with your template files in which all filenames in the template have a unique prefix.
Or
2. load epub to be merged first and rename conflicting files so that Sigil can properly handle updating and correcting all links before merging into first epub.
3. write an edit plugin that groks your template system and have it load the files and fix any broken links
BTW, this bug may still cause issues with similarly6 named multimedia or images as I do not yet have a case insensitive filesystem to check with (yet). My focus was on preventing the initial crash.
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