Missing built-in gem passives after returning (Controlled Metamorphosis, Against the Darkness)

Hello,

I've just returned to the game after a long break (last played in 3.22 Sanctum). I logged into an old character in the Standard league and noticed that the built-in gem effects from some passive skills are missing.

Specifically, these are gone:

Controlled Metamorphosis (located in the Death's Embrace cluster near the top of the tree)

Against the Darkness (located in the Shadow cluster at the bottom of the tree)

The nodes are still allocated and grant their stats, but they no longer provide their unique skill functions.

What I've already tried:

Restarting the game client.

Checking other characters - the issue is only present on this one.

Confirmed it's not a UI error - the skills are missing from my skill bar and character stats.

I suspect the issue might be related to passive tree changes that happened after I stopped playing.

Could you please clarify the situation? Is this a known issue? Are any specific actions required to restore the skills (e.g., un-allocating and re-allocating the points)?

Thank you for your help.