I walked the 'C' Nine with Linc (Tom and Wayne too) and there are a number of changes that were made due to the changes in enviornmental regulations. I would bet that much of what you don't like has to do with the restrictions placed on Linc and the club. The practice facility altered two holes all by itself.
But he was the right guy to do it, and he tried his damnest to be true to the origional nine holes. There is no intentional "Lincisms", he was committed to Flynn. His work was excellent concidering what he had to deal with.
What would I do? we have a completely intact, overgrown, CH Alison course in town formerly known as York Downs. Everything is still there (although Thompson renovated many green sites), but unfortunately it is a city park now (mounds and all). That one, I would rebuild as it was, there would be no "ianisms" added to the course. That's what I would do.
The only issue you get into is what you've got. Thompson's Bigwin Island was still in the ground at Bigwin Island. All 5,700 yards and greens around 2500 square feet. Would you rebuild that?
The 'C' Nine worked becuase it had size and length enough to fit today, most of these courses simply can not return to modern times untouched.
Linc's restored 9th on the C Nine. Damn Impressive if you ask me.