I was having the same issue, where I had around 7000+ flow files and I needed to merge them into one. Provided that, I didn't know what will be the exact number of flow files, I couldn't specify that number in Minimum Number of Entries attribute of mergeContent processor to make it only 1 flow file after merge.

After trying a lot of things, including trying to count the flow files or induce a delay before sending them off to merge, I finally found the solution on the mergeContent documentation below :

https://nifi.apache.org/docs/nifi-docs/components/org.apache.nifi/nifi-standard-nar/1.6.0/org.apache.nifi.processors.standard.MergeContent/index.html#:~:text=The%20%27Defragment%27%20algorithm%20combines%20fragments%20that%20are%20associated%20by%20attributes%20back%20into%20a%20single%20cohesive%20FlowFile.%20The%20%27Bin%2DPacking%20Algorithm%27%20generates%20a%20FlowFile%20populated%20by%20arbitrarily%20chosen%20FlowFiles

And there you go ! setting 'Merge Strategy' property to 'Defragment' and 'Attribute Strategy' property to 'Keep Only Common Attributes' fixes the problem for me.

In all my flow files, they have common attributes and are now merged into a single flow file.

The original question is from 2019, but I hope it helps out somebody else looking for an answer.