Can a parenting time order still be enforced while a child protection case is open?

Yes. An existing parenting time order made under the Divorce Act or the Children's Law Reform Act doesn't get suspended automatically just because a children's aid society has opened a file or started a protection proceeding. The order stays in force and enforceable unless and until the family court that made it varies it, or the child protection court makes its own order - such as a temporary care and custody arrangement - that changes where the child is actually living and who has authority over them day to day.

In practice, the two systems can pull in different directions for a period: your family court order says one thing, but the child's actual placement, set by the protection court, may not match it. If that happens, don't assume the older order has been overridden - go back to whichever court is best placed to sort it out, usually by bringing a motion in the family case to address the conflict, or raising the parenting order within the protection proceeding. A society has no authority to simply cancel a parenting order on its own; only a court can change it.