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You will need to add the files to Sigil (there is a menu option for that). That will also ensure the OPF file will be updated correctly. I am a bit surprised actually, because if you import a HTML into Sigil all the related files (stylesheets, images, etc) should also be imported automatically and the links adapted. At least that is what I am used to. It could be that this is not the case if you use absolute instead of relative links.
With RegEx it should be easily fixable.
With regards to the project you are working on, it will be a difficult project with high chance that it will not work on all/most platforms.
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