Apologies that no one replied to your question. Glad you got it sorted and thank you for posting a sum. I'm not sure why the input or the GeoEvent Service you published had to be deleted and re-created. I have seen this behavior back at the 10.5 (10.5.1) release when I imported a configuration from an XML and then edited an input or output to change its name / label ... but it doesn't sound like you were doing anything like that.
A debugging technique you might want to note, for the future, is that you can set the GeoEvent Server Logging to DEBUG on 'Root' for a very short period of time to try and capture what exactly is going on. The debug logs are going to be very verbose, so you'll have to open the log file in a text editor rather than relying on the logging interface in the GeoEvent Manager web application.
You can find the kafaf.log beneath the following folder: C:\Program Files\ArcGIS\Server\GeoEvent\data\log
In this case you would be looking for messages from the following logger:
com.esri.ges.transport.featureService.FeatureServiceInboundTransport
The debugging technique would be to turn off (e.g. stop) all inputs, GeoEvent Services, and outputs you have running, delete the logs (to clear out any old messages not related to this debug session), then set logging to DEBUG on 'Root'. Start the input and check the logs for anything that looks relevant. Maybe then start the GeoEvent Service and output and check the logs again. Be sure to set logging back to INFO for 'Root' as soon as you can so you do not continue to collect messages in the log file (particularly for every request over the HTTP wire - there will be a lot of those).
In this case the DEBUG logs for the FeatureServiceInboundTransport were a little help. Here's a snapshot; setting the logging to DEBUG for only the one logger made it reasonable to use the GeoEvent Manager's log viewer:

What I did for the test was leave the input's default query expression set to 1=1 to confirm that feature records were being polled. Then I changed the query expression to look for only records whose gf_imported attribute was equal to zero, so that I could see the warning that the query expression excluded all available features.
For future issues, please consider submitting an incident with Esri Technical Support. Esri staff work to try and post responses to questions on the community forum, but forum submissions do not always get answered. An incident submitted to Esri Technical Support will always be assigned and someone will work to address the issue. (You might consider opening an incident referring to a forum item you have posted to request a forum response - that would give your issue maximum exposure.)
- RJ