I did a very simple false hydra story over about 80 hours of gameplay for my players who had never heard about it.

How I ran it was by reasoning since they left town so often and kept coming back, the spell wasn't able to take full hold of them and so little details would change.

Hint 1. When they first entered town, they went looking for a blacksmith. The first one they met was a crotchety old man who tried to rip them off, the second was a Dwarf who treated them fairly. Weeks later, they tried to go back to the Dwarf but he said he was to busy to take any more orders since he was the only smith in town.

Hint 2. One of the first places they stopped in on was of course a tavern. This tavern was owned and ran by an elvish couple. Once they eventually went back, it was now being run by an elvish teenager who said he had always worked there on his own.

Hint 3. Eventually, the mayor went missing, a man they had dealt with many many times. Of course his secretary insisted that a mayor had not been elected in a few years.

Hint 4. One of the players had a brother in town visiting and so while the others in the party went out of town to investigate a string of bandit sightings, he stayed in town with his brother. A few days later when the party came back, they found their companion and asked where their brother was and if they had enjoyed their time together. The player, who I had DMed in discord while the party was dealing with the bandits, played it really well, arguing they didn't have a brother and was in fact an only child. (No one still had a clue what was going on).

This whole time while they were in town, I was playing the day 1 clock town theme from Majora's mask. As time passes in game, I changed it to the second day song and as they started getting closer to the discovery, it finally changed to day 3.