Will merging duplicates keep the oldest or latest photo on iPhone 16 Plus?

It is not documented, how Photos iOS will decide which version to keep. It will depend on the resolution of the photos or other metadata you added, like locations or image captions as well.

When in doubt, merge only one pair of duplicates at a time, so you can easily put the photo back, when Photos kept the wrong version.

Before I use the "Merge" feature I am taking the following precautions:

• I add both duplicates to a new album, so I can find them again after merging.
• I keep the Recently Deleted album empty, so I can easily find the discarded duplicate to put it back, if need be.

I got random results, when merging duplicates. Sometimes Photos kept the photo with the wrong date or location, sometimes even the version with the higher grade of compression when merging JPEGs.

I am using the Duplicates album to see all duplicates in one place, but I prefer to remain in control of what will get merged and do not let Photos merge my duplicates automatically en masse. Most of the duplicates I want to keep, because they are differently adjusted versions, for example, differently cropped versions, or Live Photos with different effects applied - for example a a loop and a long exposure.