I've now implemented this player-side (I still need to implement the editor side).
As with the changes to lemming sprites, NOTHING can be done currently. NOTHING can be done until V12.7.0. With that being said - existing custom pickup skill objects will break in V12.7.0, so you will need to update your objects, if possible, when the V12.7.0 release candidate becomes available.
Yes, this does mean two versions in a row that have required changes to these objects. This is the risk you took when you chose to use in your styles an object type that wasn't officially supported, and which I have constantly reminded people is not officially supported. V12.7.0's changes will make them officially supported, so it should hopefully be the last time you need to change them - effort will actually go into minimizing breakages with them in the future, because they'll now be an officially supported feature.
To understand this explanation, you'll need a reasonable idea of how the new animation system works, as this builds on that.
Basically - pickup skills are now defined with the primary animation's name set to "*NULL". This is a special name that tells NL not to load any graphic for that animation. The only other property that needs to be set for the primary animation, is the offset coordinates and/or Z index (if applicable).
NeoLemmix will auto-generate the primary animation based on the lemming sprites (or in the case of the disarmer, a global graphic that cannot be customized). The graphic for each skill's sprite will be 24x24 in size, and as mentioned above, you can use the OFFSET parameters to reposition it. You can have an always-hidden secondary animation called "ERASE", which if present, will act as an eraser mask for these autogenerated sprites. This mask should be 24x48 in size; the upper half represents what will be erased when the skill has been picked up (more often than not, you'll probably want this to be a full erase), while the lower half represents what will be erased when the skill hasn't been picked up (you might use this, for example, to crop the image to the boundaries of your object).
Anything outside of that, you use secondary animations (most likely with the "EXHAUSTED" trigger condition) to achieve.
I think it will be a lot easier to understand this with an actual example, so I've attached a copy of what the new default:pickup looks like for V12.7.0 (graphic files and NXMO file). Of course, part of this relates to its recoloring.
If there is any effect you want to be able to achieve, that's possible currently, that you think might not be possible with this system, other than providing outright custom lemming graphics instead of using the level's lemming sprites (as I've said - I will consider this when someone shows me an actual justified use case for it), please bring it up now. I will be much less willing to adjust the system when it's already been released, than to make changes before any release happens.
EDIT: I've attached images showing the actual spritesheet NeoLemmix generates (when using the default sprites) for the primary animation of a pickup skill. As new skills are introduced, or the order is changed, this will adjust automatically.
The first version shows how the sheet looks without any erasing applied (note that in practice, when no eraser is given, NL will fully erase the 1st, 3rd, 5th etc frames - these represent the graphic after the skill has been picked up; I excluded this from the image here to illustrate better how it works).
The second version shows how the sheet looks when the default style's pickup skill's eraser is applied to it. Note that the 1st, 3rd, 5th etc frames are fully erased, whereas a circle area in the middle remains unerased for the other frames.
Finally, the cropped screenshot shows why this erase effect is important, and what pickup skills would look like without such an effect.