jahmiann, I checked the version 1.0 and I saw that, when the battle starts, a giant mushroom appears, blocks the passage and you can't use the pit until the battle ends. I mean the pit that leads to the external area. There is a relay that activates the message
"YOU EAR A NOISY CROAK COMING FROM THE FIELD: KING FROG APPEARS!".
The same relay activates the giant mushroom too and you won't be able to reach the underground any more. So I can't explain how you could go down to the pit
Anyway, if you did that, you are trapped because the grapple has disappeared. You have to reload.
After killng the boss, you can come back to the enchanded forest. Using the pipe you'll be able to shrink down and visit the boot house whenever you want. Grapple and portable pit will appear in the same place where you found the first time.