I created my PC as a chanter and any chanter get to choose in level 1 two starting abilities, one chant and one invocation I chose "And Hel-Hyraf Crashed upon the Shield" as my invocation, when I got the chance to upgrade it I did with "The Shield Cracks".
When I tried to retrain my PC I lost both the upgraded version and the starting one, so at level 1 I have no invocation and I lost one skill point because of that.

screenshots to show that

https://imgur.com/a/QTF1FH9

Same to me, My Votary (Mnk/Pld) @ lvl11 I tried retraining and lost swift Strikes. Which means I lose 1 skill point overall.

When I stopped to think about how the bug works I understood that this is probably an old bug and not a 1.2 one and that's why the developers didn't answer to this post.

I think that whenever an ability is overridden by another this will happen because they remove your old ability and replace by the new improved one but then the game has no information of what ability you had on level 1 when you retrain your character.
I don't know how they will fix this bug without giving us level 1 retrain and if they do we will be able to change our starting abilities but if I remember correctly this is something they didn't want to give us, they wanted to have our level 1 be static.

Level 1 retrain would not only solve the issue but would be more convenient and I dare to say logical. 

Edited July 4, 20187 yr by knownastherat

On my skald. I still lose my chant selected at level 1 if I retrain.