So it sounds like youre saying that you accidently tossed your unfinished prototype tool. If you talk to the NPC, they only give you the lowest level base tool. But having or using the tool isnt required to proceed with the research. If it was your only tool for that job you may need to craft or buy a new one to use temporarily. But none of this would have affected your research level. If you open blacksmith on the research tab it should show you exactly where you left off and how far you are to the next phase. When you finish that phase youll get the new .6 tool and can go back to getting bonus points with it.