Pin seen as a clock in TimeQuest but is not a Clock

I31out0 is your clock and is a feedback output from comb logic involving GND. I think this has fooled TQ.

Thus you have actually a timing path (from Q output of your registers through the xor logic and back into register clock port. I think it is more appropriate to declare generated clock as you are dealing with gated clock. The best way to see examples at TQ resource centre.

An alternative safer way is to clock both registers on clk then use I31_out0 as clock enable

Thanks, I'll look into that. I have never dealt with generated clocks before so I guess I have a lot of research to do.

Notice that even with generated clock you are likely to have serious timing violations due to the very long comb path. As I said a clock enable approach is best in your design if it is ok functionally and even then you may have to face the challenge e.g by adding more pipeline registers.

What is a clock enable approach?

Connect master clock to all registers. connect I31_out0 to the enable port of those registers which you have clocked by I31_out0. That way the enable is synchronised to master clock. The only concern then is that enable may be very much delayed. Try it first and let us see.