From what I understand, archiving an ad unit does NOT prevent it from serving ads. It is merely a way for publishers to organize their ads and differentiate active from archived ad units. I highly doubt it has any use beyond that.

As for the TOS, I really don’t know, so I’ll leave it to more experienced experts to answer that question.

Removing a below the fold ad does not violate the ToS. Marking an ad unit as archived does not violate the ToS. Which part of the ToS are you particularly afraid of?

Two weeks seems to be a lot of time to remove one ad unit. I assume the site is static in nature? You might first look in the possibilities of your hosting to use a scripting language to serve your pages. It may be a little more work add some scripts to your pages (PHP, ASP, SSI or whatever is available) to include the Google AdSense code but it will pay-off later if you want to make additional changes to your site.

Indeed @lammert
It's not normal to be editing 1000's of pages manually.
Usually you do a php include of the file with the tag and in case of removal or changes you edit 1 file once.