"To remove any lumps" means to get rid of any small, uneven or clumpy pieces or bumps in something, such as a mixture or a substance, by making it smooth and even. Full definition
Another reason not to remove the lumps for aesthetic reasons is that they can grow back meaning that the discomfort for the dog really was in vain. (healthguidance.org)
Make sure to fluff up the ingredients to remove lumps before measuring and sift the cocoa powder before measuring. (lowcarbmaven.com)
If you have any trouble removing lumps, an immersion blender is a great tool that can quickly smooth it all out! (kitchenistadiaries.com)