Pam,
I am not sure why the renumbering is not working, since you state that the correct chapnum building block is in the autonumbering format.
Anyway, in the preferences, there is an optional checkbox labeled Remember Missing Font Names, which I keep checked; however, you can uncheck it if you are sure about things. BUT you open a file that uses a font you do not have, FrameMaker displays the message about unavailable fonts. IF you have the option about remember missing fonts CHECKED, then FrameMaker allows you to edit the document, even though you do not have the font. When you save and close the document, the document still uses the missing font, even though the initial message states that it is reformatting with a different font. So, when you open the document again, the font is still missing. IF you UNcheck the preference, then FrameMaker WILL reformat with a different font and you will not get the message the next time you open the file. So, you can get rid of the message by unchecking this option, but it may not be what you want or should do...
In a structured document, your template and EDD control the formatting. So, your system should have all the fonts required by the template and EDD. If not, then I would think you should get them.
Now, when you convert an unstructured document to structure, sometimes a few "bits of fluff" remain in the file. So, there may be a font change in the file that does not have any text associated with it. If so, FrameMaker sees this as a missing font. Once I get a file converted to structure and fix everything so that the file validates and everything else looks good, I open a new, blank template file. Then switch to the structured file, open the structure window, select the root element (the one highest in the hierarchy), copy it, and paste it into the blank template. Then I save this file with the same name as the old one or with a new name. This file should have all the detritus in the old structured file removed. This is also a good way to standardize your color definitions.
The warnings about the inconsistencies in the color definitions should cause few problems, except in the display of color, but they certainly should not affect the numbering problem.
If you do the clean up I suggest above with all your newly structured files, maybe that will be enough to correct the numbering problem, but that is just a guess. If you have done all that I have presented in earlier posts, the numbering should work correctly.
Good luck,
Van