Every one who's spent significant time travelling by boat hits this issue. You can minimize the risk by constantly carrying the portal mats and throwin' one of those down at your 'exploration' hut. It's a little gamey, but if you have a dedicated 'temp'/unnamed portal whose only purpose is to be your 'exploration point', then theoretically you always have a way back to your main base.

Once you realize the portal's location might actually be useful, use a different base portal and set it to the new location's name. Travel back thru the 'temp'/unnamed portal, and rename it to the new location name and put that name on your map. Later, you can dial any of the three/four travel portals to that name/location and go back there...

Kinda like making sure you eat well before battle, this game encourages you to set-up before you do anything major...