Ouch! I had to do this one time and luckily it wasn't a very complex assembly. The method I used to go about it is still tedious though.
Essentially, I saved the imported part as a different part name for each component in the assembly. Then I redefined the imported geometry (in each component) to delete the appropiate surfaces in order to get the part model. Then I built the assembly by aligning the CSYS in each of the new models.
Like I said, VERY tedious & somewhat time consuming, but luckily, not a lot of parts or even complex geometry.
I have heard of other 3rd party software (e.g. CADfix) that can do what you want, but I don't know enough about them to guarantee results.
Hopefully, another user will have a better alternative than mine.
And that the accepted solution in the mentioned thread was mine! Kewl!
Concerning the colours: if you want the generated parts have the same colour as the imported quilts, do the following in assembly: choose from the appearances menu #modify from model and select one of the coloured imported quilts. Choose #ok. Now select the part created from that quilt and choose #set. Somewhat time consuming when you have many parts with many different colours, but the colours are at least the same as the import.