old site hyperlinks

I put a lot of hyperlinks between products and information pages in my first store.
Now I as try to absorb in my mind this partial upgrade from 1.27d to 1.3.5, I discovered that all the products hyperlinks (from DB upgrade) I made are still pointing to the old site.

Should I leave these alone for now, and continue with my comparison of files, (yes, I know this should be done first) and then wait until I change my config files "domain_name /newshop/" to "domain_name/catalog" again? I "assume" that would make all the hyperlinks work again. Or is there a better plan to deal with these things for the future.

Gee, what if I move this sight to root someday, then all the hyperlinks would be wrong again? Did I set myself up for extra work?

I am mostly building again from scratch with the attempt at not moving over all my old mistakes.

Any thoughts or a better plan for a new store is much appreciated.