The way parenting orders work is that once they are made, they become the default arrangement. If Mum and Dad agree to do something other than what's in the parenting orders, that's fine (and kudos to them!), but unless they file the changes as new consent orders, then either parent can refuse to agree, or they can renege on what was agreed, which reverts both parents back to the original parenting order. Parenting orders can only be invalidated by new parenting orders.
So the short answer is that no, an agreement between the parents does not invalidate a parenting order. The only way the parenting order becomes invalid is if new parenting orders are filed with (or made by, in limited circumstances) the Court, or when the child turns 18.