Splunk support did contact me this morning. We weren't able to determine an exact cause of this behavior, but did find that stopping the Splunkd process caused it to stop hanging. Specifically, the command prompt window where I had run "Splunk offline" displayed a message indicating that primaries had been reassigned and it was complete. I set the splunk service to start manually, rebooted the server and then installed the Splunk 6.4.6 update. It appears to be working now - it rejoined the cluster and I have not seen any signs that there is a problem.
*** I'll accept this as an answer with a caveat. I recommend contacting Splunk support in this situation, as they may identify something in the splunkd.log that points to a root cause, or may indicate that you should not terminate the process like I did ***
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