When the Better Together Update came out, I converted my world over to the Bedrock Edition, this world has two portals with centers located at x = 0, y = 41, z = 0, one in the Nether, and one in the Overworld, each of which is three blocks tall by three blocks wide, and both portal frames are oriented in a north-south direction. Prior to world conversion, these two portals linked to each other perfectly. Now, the two portals fail to link to each other on a mutual basis, with the portal in the Overworld linking to another portal, at completely different coordinates, while traveling through the one in the Nether generates a new portal in a nearby cave system.

I know all about the Nether to Overworld coordinate ratio and how the change in that ratio simply throws everything off, but because the coordinates of both portals are a perfect match in this case, I know that this issue has nothing to do with that. I suspect this has something to do with the portals being located across chunk boundaries, that, or there's a failure in the exclusion-zone physics of Nether Portal linking.

HOW TO REPRODUCE:

On Xbox One Legacy Console Edition:

1: Build your first portal at roughly 200-300 blocks away from x = 0, z = 0, don't build it too far underground.

2: Locate the x=0, z=0 coordinates.

3: Build and activate a second, 3-by-3 nether portal with the center of the portal a x = 0, z = 0, at a very different y level, preferably significantly deeper underground, and take note of that y level.

4: Travel through the first portal that you constructed and make your way to the x = 0, z = 0 point, making sure to match the y level of the second portal you constructed, make sure the portal you emerge from is on the same sides of x = 0, z = 0 as your first portal.

5: Build and activate a second three by three nether portal with the same orientation as the one located at x = 0, z = 0 in the Overworld.

6: Travel through this new portal and observe that the two portals at x = 0, z = 0 link up perfectly.

On Bedrock Edition:

1: Convert the Xbox One world where you completed the previous steps to Bedrock Edition; if MCPE-25354 doesn't overwrite your testing area, you can proceed to the next step.

2: Test out the two portals at x = 0, z = 0 to see if they work.

3: Observe the results.

WHAT IS EXPECTED:

The two portals at x = 0, z = 0 should link up perfectly.

WHAT ACTUALLY HAPPENS:

Either 1) one of your portals at x = 0, z = 0 links up to your first set of portals, or 2) a new portal is generated.