The Republican party's proposed rules package was presumably modified, in writing, to reflect those backroom deals. That proposed rules package however has to pass by a majority vote. (The Democrats also have a proposed rules package, but it is presumably dead on arrival.) If the rules package proposed by the Republicans doesn't pass as-is, the proposed changes to the rules from the previous Congress (and any new proposed changes) can be dealt with on a one-by-one basis.
The metarules for how the rules are set are nearly set in stone. The new House cannot change those metarules until they have agreed upon the rules themselves. To establish the rules for the new Congress, the new Congress has to live with the old metarules, some of which are very, very old.