I had a problem where optimization would take out gates I wanted to stay, no warnings.
That was with all optimization off, at the time, ~ 3 years ago, no way to resolve the issue.
I would post this on Cypress.com PSOC forum, there may be a way to
defeat warning and make sure no nets are broken or to force particular
net routing.
Of course you could always eat a pin or two and route so tool does not know you
have latch loop........create the "net" externally.
Regards, Dana.