Isolated bold, underline or italics can be preserved as character styles BEFORE you apply paragraph styles. You can do it using Find/Change one at a time for the attributes, or the scripts in the first link I gave you above will automate it. Work on a copy of the file for safety.
If you aren't interested in doing a proper cleanup and you cannot figure out something usnque abou tthe types of paragraphs that need different indents (so you can use Find/Change), you'll have to go through paragraph by paragraph fixing as you go.