Nanding,
If the general intent of the contract is to keep responsibility of the means and methods on the contractor then the contractor shall be allowed to make any changes to the schedule he deems necessary. In this case the approval of the schedule shall be with regard to many other requirements that are independent of the logic as long as it is reasonable. Under this type of work if the specifications are in conflict with the general intent of the contract it is the general intent that shall govern. The contractor keeps control on the means and methods but is responsible to keep informed the owner.
It is common for some specification writers not to understand that scheduling specifications shall be adapted to the general intent of the contract. Many pick up old specifications from the desk without taking the time to analyze them. Scheduling under traditional contract type is different as scheduling under the different type of PM agreement as well as on jobs where the contractor is to follow a schedule as issued and controlled by the owner or his rep.
If the specifications are in conflict with the general intent of the contract this usually does not invalidate the contract or the specifications but just the portion on the specs in disagreement. How you shall react to this requirement depends on your contract as a whole.
Mike's advice is very wise and practical, at home it is common for us to follow two versions as many of the specs do not allow the contractor to make changes in the logic of the schedule until approved. This is frequently in contradiction with the general intent of the contract but gets complicated when changes or delay claims are still pending. Our versions are in general a good representation of our plans as malicious manipulation can backfire and make you unable to make a valid claim.
We start with the updating of the schedule of record and transfer performance data to the action schedule at a single click of the mouse, it is easy, error free and only new activities not yet in the schedule of record must be updated.

Just find the equivalent functionality in the software no matter if imposed or of your choice.
Regards,
Rafael