Ask your DM
For reasons I'm about to go into, it is up to DM adjudication whether or not you are able to retrain Darkness, or whether you still retain the ability to cast it using Sorcery Points afterwards.
It is unclear whether Shadow Origin Sorcerers may replace Darkness with another spell
The evidence for this is somewhat unclear, since there's no general rule that states whether or not spells learned through class features may be unlearned or not. There are, however, many features that grant additional spells to a character that have varying rules about whether they may be replaced or not.
For example, Divine Soul Sorcerers' Divine Magic feature explicitly allows the spell learned from the feature to be replaced:
In addition, choose an affinity for the source of your divine power: good, evil, law, chaos, or neutrality. You learn an additional spell based on that affinity, as shown below. It is a sorcerer spell for you, but it doesn't count against your number of sorcerer spells known. If you later replace this spell, you must replace it with a spell from the cleric spell list.
—Divine Soul Origin, Xanathar's Guide to Everything, pg. 50
Conversely, the Bardic feature Magical Secrets is not explicit about allowing spells to be replaced, but is commonly interpreted to permit spells learned to be retrained later
By 10th level, you have plundered magical knowledge from a wide spectrum of disciplines. Choose two spells from any classes, including this one. A spell you choose must be of a level you can cast, as shown on the Bard table, or a cantrip.
The chosen spells count as bard spells for you and are included in the number in the Spells Known column of the Bard table.
—Magical Secrets, Player's Handbook, pg. 54
However, it's commonly understood that the extra spells gained from a Ranger's Archetype may or may not be eligible to be replaced because of minor differences in how the feature is worded.
The Eyes of Darkness feature says you learn the spell Darkness and become able to cast it with Sorcery Points, but it doesn't say you "know" it, which appears to be a sticking point for the Ranger example:
When you reach 3rd level in this class, you learn the darkness spell, which doesn't count against your number of sorcerer spells known. In addition, you can cast it by spending 2 sorcery points or by expending a spell slot. If you cast it with sorcery points, you can see through the darkness created by the spell.
—Eyes of Darkness, Xanathar's Guide to Everything, pg. 51
So whether or not the Sorcerer can replace this spell might very well come down to what their DM says about this rule.
"Okay, but what if we assume they can replace Darkness with another spell?"
In that case, if the Sorcerer retrains this spell, they probably lose the ability to cast Darkness using Sorcery Points. The feature says you learn the Darkness spell, and then gain the ability to cast "it" using Sorcery Points. This ability probably does not persist beyond retraining the spell, since the spell you gained the ability to cast with sorcery points is no longer a spell you know.
It's a tricky corner case though. The feature doesn't expressly say that casting-via-Sorcery-Points is contingent on retaining the spell, but it also seems from context like the feature is simply assuming you'll never unlearn the spell. That could be evidence that the spell cannot be retrained, but the feature doesn't expressly say it cannot.
The feature doesn't expressly say that Darkness cannot be retrained; and if it is, the feature doesn't say what should happen because it has been trained away. It's clear from context the feature is assuming the spell is not retrained, and my sense is that this is probably not an intended use of the feature.
At my table, I usually rule that memorized spellcasters can retrain spells learned from subclass features, but because of how this feature seems to assume the spellcaster will not do that, I don't think I would allow it. That's just my ruling though based on the weirdness that this situation might create, so any other DM considering this specific interaction will need to decide for themselves.