If you are losing the local formatting overrides, you must be applying the paragraph styles and telling ID to remove local formatting. That said, the best approach here is probably to assign a character style to each type of local formatting and apply it to the text before applying the paragraph styles. There are actually a few scripts floating around here that will do this for you -- parse the whole thing, find variations, create a style, then apply it as necessary. One of the best is Jongware's preptext. See http://forums.adobe.com/thread/429756
Thank you so much. You have just solved a rather large problem for me. It was preventing me finishing a contract.
A huge relief to find that it can be done and that someone has been kind enough to spare time to help.
Many many thanks
A very happy Matthew Hague
Jongware's script is excellent, and free!, but it only finds a small
number of local overrides.
If you want a script that will find ALL possible overrides, take a look
at my "Create Character Styles from Overrides" script:
(look under the "Scripts" menu).