I have experienced that in the past, too. I believe that I have recently found a work-around that seems to consistently work. It sounds like you are importing a Word html file which creates the worst html code on the planet. The process I use is to load the html file into BBEdit and then run
Tidy - Clean Document with the following options checked: Eliminate Bogus Markup, Discard Empty Paragraphs, Discard Comments & Optional Tags
Tidy - Reflow Document with the following options checked: Wrap Attributes, Indent Attributes
In BBEdit the Tidy commands are located in the Markup menu or palette. Shortcuts can be set to make the process pretty quick, too.
This will create very clean code. I also change the encoding to UTF-8 and make sure the Doctype is Transitional 4.0.1 before saving the document. Any other Doctype will make the file unselectable in Accordance when attempting an import.
This will import pretty easily into Accordance. If you want Section links in the Accordance file, the sections can be formatted with headers while in BBEdit.
I have imported some pretty significant size files using this procedure without having any of those Bolding issues or the hanging indent issue.
Other software that offers similar functions might work too but BBEdit is hard to beat for this type of thing. It sells for $49 in the Mac App store or at barebones.com. A free downloadable demo is available at the Barebones website. I have used it for many years and find it essential.
Hope this is helpful.