Two clocks are synchronous when their relative phase is predictable. This is usually the case when their tree originates from the same root in the netlist, and when they have a common period.
For example, a generated clock and its master clock that have a period ratio of 2 are synchronous because they propagate through the same netlist resources up to the generated clock source point, and have a common period of 2 cycles. They can be safely timed together.