The big problem of formal verivication. Because, such tool (like Mentor FromalPro or Synopsys Formality) compares input logic for each register between RTL and gate-level netlist. If you asked Synthesis to re-balance logic, the input logic for some registers will be different. For Synopsys Formality, you can use side-file .svf, which is generated by DesignComiler and help Formality to verify such design. Still, it is complicated for tools to verify re-balanced (re-timed) designs.