A day on a Eurail pass is usually one 24 hour period. Travel commencing within that 24 hour period uses up one day on a Eurail pass.
Europe train passes, like a Eurail pass or Eurail Flexipass, come with the option to choose a number of travel days. Three days on a Eurail pass means three twenty four hour travel periods (usually) commencing at midnight, not three train trips.
If you've chosen a Eurail pass with three flexible travel days over, say, two months, you can use those three days at any time within those two months. If you like, you can travel to two or three cities in one twenty four hour period.
What's a Day on a Eurail Pass?
A twenty-four hour period on a Eurail pass generally starts at midnight.
If you board a train before 7:00 pm that does not stop until after midnight, you're still on one day. If you board a train before 7:00 pm for, say, an overnight train trip, and then change trains before midnight even though you're still traveling after midnight, you will use two of the days on your Eurail pass.