The upgrade length depends on many factors, starting FW revision, controller type and IO / connection load on the group/members.   You're longest upgrade will be from 4.x to 5.x.  After that will get better.   The website has a PDF "Operating system considerations" that shows how to update the Windows Disk Timeout value to better tolerate restarts/failovers.  If you haven't made that registry change you will need to restart the server to make it effective.  Also some applications, like SQL and Exchange can be more sensitive to the restart timeout.  The upgrade process, reprograms both flash cards, then restarts the passive CM and waits for it to come back online.  Then the primary will failover to the passive and become the active CM.   Finally, the now passive CM is restarted to complete the upgrade.   4.3.0 -> 5.0.8 ->5.2.1   5.0.x->5.2.1  There are some very important fixes in 5.2.1 that you should avail yourself.   Are these in the same group?    At the very least you want to do this during a quite IO period, if a maint window isn't available soon. 
Greetings: I have 3 EQ6500x shelves that are all on different firmware revisions: 4.3.0, 5.0.2 and 5.0.7.  Question: is the firmware upgrade process seemless and without interruption?  In other words, should I plan for an outage during the upgrade or can the upgrade happen "during the day" without notice? Ron Gage  
EQ6500 Firmware upgrade