Because of the amount of work entailed in having them changed by a third party.
Find the ones you can control and change them- review any link submission, directory submission etc- software that may have been used, for a list of these that you did unintentionally.
Focus on the other recommendations that I made, and then restart your manual submission process, for obtaining HIGH quality links. The majority of these links/ directories etc, will be ignored by google- as they are low quality. Yet I do notice that these are pretty specific to your industry.
These could be scraper sites, which scrape your content and then add a link - because these have been hit by algorythm updates, more than likely they are strongly devalued anyway, but they can appear to be purchased links on your end, which gives the appearance of breaking Google's TOS.
Apply a copyright tag, publisher and author tag on your new site as well to avoid this abuse from scaper sites in the future.
There is no short cut, you have a lot of work ahead of you- I don't envy your situation, but I have seen much worse.