I don't know what it is, after importing my save I seem to be missing a lot of the abilities. All of the convert x damage to y are gone, sword throw options never come up anymore, additional damage x as %y, and so on. Most of what I have as an option are flat increases to damage, percentage increases to damage, critical multiplier, and that's it. At first I thought this was an update or something to clear out a lot of the superfluous stuff but I'm not sure anymore.

If you start a run then you should get a lot of the abilities right back. I did remove a number of ability mods that did not fit the game design. Let me know if you still have an issue