freeze root of all design after every change in it

With that older version of Quartus, you can use incremental compilation. If you find that part of your design is meeting timing and not changing anymore, set it as a design partition and then set its netlist type in the Design Partitions window to Post-fit, essentially locking down that part of the design by reusing its post-fit netlist. That way, on the next compile when you try to change or fit other parts of the design, you'll save compile time and maintain performance on the part that was "locked down."