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Unfortunately, without a test epub or more details, we can not easily help. Repairing links to external resources should have no impact on Sigil. Having multiple epubs should not crash anything in Sigil either. The op problem was he had a totally incorrect guide item that said his main book chapter was actually the toc and that confused Sigil as it tried to rebuild the toc but could not as a result of it being the only main chapter. More likely, you are seeing the last bug we already fixed when deleting an empty file that was cached for use by the Preview if enabled.
If you can post a sample epub and pm me with the exact steps to recreate the issue (as the op did), I would be happy to look at it.
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