Thanks for your suggestions.
Since the changed netlist comes from FrontEnd they are unaware of the physical attributes, like placement. During the eco process, it is possible to place them in an appropriate location using ecoPlace and/or other commands in order to satisfy their timing requirements. However the only missing part is the connection of the clock pin of the flop to the appropriate level in the clock tree.The netlist might tie the CK pin of the flop to the module/main CLK.
There are other tools in the industry which automatically identifies the level in the clock tree to which the newly added flops are to be connected to meet the timing requirements. This feature is part of incremental/eco CTS. Hence was wondering if there's a way to accomplish the same using encounter as well.