Annorax was not trying to restore the timeline, and could not restore the timeline just be continually subtracting more and more matter, events, persons and confluences...
What he was trying to do was restore the borders of the Empire, and possibly the size of the population inside those Borders, no matter how unfamiliar and strange the history was that brought the Imperium to that familiar state as long as they dominate or decimate their neighbours.
Which is a lie Annorax tells the crew... He just wants his wife back.
Seriously though, what did he think was going to happen the first time they used the weapon? She could have survived and never met or fallen in love with him, or she did meet and fall in love with Annorax who is now just another dude hanging out in the new universe married to his wife.
Ridiculous that the leaders of the Krenim would sign off on this.
Being murdered as history rewrote itself.