You may want to look in to using the "Wait" and "Notify" processors to accomplish this. The Wait processor would route a FlowFile to the wait relationship (default configuration) until a release signal is written to the cache service by the notify processor. So you route one file to wait and the other to Notify.
Do you know what order the files will always arrive in? If files arrive in no specific order, you may need two wait/notify sets of processors. One flow path has a wait feeding a notify and the other a notify feeding a wait. That will result in a wait occurring on either FlowFile no matter which file is received first.
When an "Answer" addresses/solves your question, please select "Accept" beneath that answer. This encourages user participation in this forum.