I installed Pergo in my kitchen,living room and dining room. If you think the floor/subfloor underneath the Pergo is damaged from water my guess if you have to let it air out and determine if it needs to be replaced. My favorite product for getting out moldy smells is bleach but there may be something better/safer for use on your subfloor.
Re: Replacing the planks - which I have done - its not fun. First, I applied adhesive remover ($2-$3)to the seam. I think it helped a little but I ended up pulling apart and using a hammmer to break out the rows of damaged boards - which was not totally smart because I ended up replacing more boards than I intended. Then I applied the adhesive remover to the tongue/groove of the remaining "good boards" and scraped all the excess glue out with a putty knife. When the remover dried (overnight)I installed the new boards. For imperfections I used some filler (Pergo brand). I just completed the job about 2 weeks ago.
Don't forget to put down 100% silicone caulk around all the expansion spaces (between wall and Pergo). I also installed quarter-round trimming in the kitchen.
Depending on the size of your kitchen, it may be easier to replace entire floor than repair the boards after you get the floor/subfloor taken care of...and the dishwasher fixed. Don't forget that caulk! Good luck!