It should work with any image regeneration plugin (for example Ajax Thumbnail Rebuild or Regenerate Thumbnails). Both are great and work basically the same way: regenerate different image sizes (and replace existing once) using the original, full size image.

So if you have full size image without watermark applied it will generate new images without it (and personally I suggest that). If you apply watermark to full size images, image regeneration should create smaller image sizes with a watermark applied.

I think it’s much safer to keep full size image intact (without watermark) and bulk watermark regenerated images (in case you need to change something in watermark settings)