Synchronization Chains not detected

Yes. By default Timequest will examine the relationship between all the signals, including those that come from different domains. You can restrict this by creating groups, and then Timequest will ignore all the signals crossing from one group to another. But of course this means that you need to be sure that ALL the signals that go from one group to the other are properly synchronized.

So in your case, if you place the clk250Mhz in group A and clk200MHz in group b:

set_clock_groups -asynchronous -group { clk250Mhz }
set_clock_groups -asynchronous -group { clk200Mhz }

You can put several clocks in the same group, for example if you have a 100MHz output coming from the same PLL than the 200MHz clock, and signals crossing from one to the other without synchronisation, replace the last line by:

set_clock_groups -asynchronous -group { clk200Mhz  clk100MHz}

All the clocks that you use in your design should be in one group. At least for the sake of clarity, I don't know if Timequest places automatically all the remaining clocks in another group.