minecraft-java-edition
In my singleplayer survival world, I built a large underground base, and stupidly decided to put my nether portal in it at about y=10. I ended up being stuck in a nether cave underneath huge amounts of lava. I built another portal on the surface, but since it's within 128 blocks of my first one, it goes to the same place.
If I place water next to the lower portal to deactivate it, if I then use the surface portal, will it take me to the surface in the Nether? If not, what should I do?
First, take note of some information about light-emitting blocks from the Minecraft wiki:
This means that if you wanted to light up a horizontal line of blocks such that the light level was 8 or higher everywhere on the line (to prevent most hostile mob spawning), you could place torches along the line with 12 blocks between them, or glowstone blocks along the line with 14 blocks between them.
Now, moving vertically will decrease the amount of light as well, also by one for each block moved. This would mean that if you moved 3 blocks horizontally, then 3 blocks vertically from a torch, the light level will drop by 6 to a value of 8. So, you could just count the number of blocks you have moved both horizontally and vertically from a source to figure out what the light level has dropped to and when you need to place another light source. I believe once you reach a count of N-1 blocks from the light source (where N is the light level of the source) is when you should place another one.
A potentially easier alternative to counting is to use the debug screen (press F3) to track light levels. This will show you a bunch of stats, like so:
The number to pay attention to is the one I circled labeled "bl", which stands for block light. This is the light level due to sources other than the sun and the moon as measured at your head level. This means that if you place a torch on the ground, then stand in the same spot, you will get bl = 13, since your head is one block above the light source.
Using this may make it easier for you to lay out your light sources and to check where you may have some dark spots. I use it often inside my structures to make sure I have lit them up appropriately.
This is how it works:
Every time you enter a portal, the game looks for an exit portal inside +/-128 blocks square (y is irrelevant). If you enter a portal at x=100, y=60, z=200 in the overworld, this corresponds to x=12, y=60, z=25 in the Nether. The game scans a square from (x=-116, z=103) to (x=140, z=153), for all y values from 0 to 128. The closest portal in that space is where you appear. If there is no portal in that area, one will be created in a suitable place. Since there is a chance the x=12, y=60, z=25 will be obstructed, the game will search for an open space in that +/-128 blocks square. If such space is found nearby, all will be good, the new portal will lead back to the same one in the overworld.
Note that the game will only scan within the map height. That means that if you place a portal above the nether ceiling, it won't be found, and the game will create a new one for you.
However, sometimes the game will put the Nether portal far from the starting point, if it can't find other suitable place. Let's say it puts the Nether portal at x=80, y=60, z=110 (this is still in the +/-128 bounding box). When you enter that portal the game will search the corresponding space in the overworld: starting from x=640, z=880, it will search the +/-128 blocks - from x=512, z=752 to x=768, z=1008. As you may notice, the original overworld portal is well outside this box. So the game will create a new portal in the overworld. This is what is happening in your world.
To fix that, write down the coordinates of the portal in the overworld (use F3 to get them) and divide them by 8. Enter the Nether, go to the calculated coordinates and create a portal from the Nether. You don't have to be exact, as long as you are within 16 blocks from the calculated coordinates (you need to match only x and z, y is irrelevant). Then the game should find the original overworld portal. Or: Move the overworld portal using the above logic.
In described situation, there is no way to make the two portals lead to each other without moving either of them. I'd move the nether portal and if the new position is outside of the fortress, I'd build a short safe walkway to the fortress.
Here is a crude drawing of the process: 
Best Answer
Break your bottom portal in your world, make another portal up above, then go to the nether with that one. Go to the bottom portal and deactivate it by breaking it, and then finally go back to your upper nether portal in the nether and use it, taking you back to your world.