You actually didn't lost a thing, except the placed ones, when it goes negative, it means that you have extra points (you can see by the counter).

When the bug happen, the trees you reset come back together with the new acquired ones, hence the negative points, to fix you need to do a full reset.

It's like you over leveled your base level (virtually), on the image above, my Sin is Lv 60 but due to the bug, it's like I have a Passive Tree of a Lv 80 or so.

To avoid it, you have to reset a tree (just one), close the window, and open again, assign the points you want, close the window, reset the next tree, close the window, assign the points you want, and so on and so forth.

It's a pain but it's working so far for me, I was doing this with all the trees I wanted to reset, but it suddenly happened (the sample snipped above is the result).

One of the staff said on another thread about this that they will look into it again, hopefully by next patch we have a definite fix.