In the original Rune Factory, when playing my first game in order to create my Guides, I defeated the Sechs Army at the earliest possible opportunity. Although I then was able to add detailed information about Freyr's victory to the Guide, the situation had some unfortunate side-effects.
For example, I no longer was able to complete the Stoller Chalice Quest. For a long time, I did not understand WHY I could not trigger the rest of the Events in the Quest. Initially, I believed that maximum FP was the solution, but even with Sabrina, Neumann and Nicholas at 10 FP, the Quest would not move forward.
In fact, you cannot complete the Stoller Chalice Quest AFTER you have defeated the Sechs Army. I believe that the reason for this mirrors that of the situation when you obtain the Pass for Carmite Cave from Godwin on the second day of the game.
When you do not have a Pass for Carmite Cave yet, you can speak to Mist on 3 Spring when she comes to your farm at noon and she may offer you another bag of Radish Seeds. When, however, I cleverly tilled 100 squares of my field on 2 Spring in order to obtain the Pass from Godwin immediately on the 3rd, I then experienced a very different dialogue with Mist.
She only would refer to my achievement in obtaining the Cave Pass... No more offers of Radish Seeds to a struggling new farmer!
In the case of the Stoller Chalice Quest, you need to speak to Sabrina in her house after hours BUT if you have defeated the Sechs Army, her dialogue changes and she only will praise your victory.
There may be other occasions in Rune Factory where an early success in unlocking a Cave could prevent an essential piece of dialogue. I will try to pinpoint any others that I discover.