Problems assigning AD groups to sharepoint sites

While doing a project this week we got a really bizar issue that users couldn't acces their sites anymore.
The situation was as followed:

• User user1 was in group group1
• Web web1 had unique security (not inherited from its parent) and group1 had Read rights to that web

There was one problem though: every night there was as batch job that recreated all the AD groups for our company, instead of updating it.
This resulted in the groups still being added on the web, but the internal SID they referred to did not exist anymore.. thus blocking all the users from their sites.

Possible solutions:

• Update the AD groups instead of deleting and recreating it prevents the problems from ever occuring
• Update your security on the sharepoint webs through a timerjob after the AD creation batch has complete (not recommended!)