Update whatever product management extensions you have checked in to ensure they're compatible with 5.9. Your clients could absolutely care less what version of ePO you're running. Nothing in that upgrade is going to change anything relating to agent communication what-so-ever.
Please go through KB71825 to ensure you are ready to upgrade. Also run the pre-install auditor tool to identify any issues.
KB87673 is also the 5.9.x known issues KB, please review it before upgrading. Be familiar also with how to migrate the sha1 certificates to sha2 so no communication is broken. That is documented in the 5.9 installation guide.
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