How to go about Cheque bouncing in case of stock dispute?

Dear sir I was dealing with an appliances company and took distribution for the same in aug 2017 . I have two cheque s as security as trade practice with filling of distribution opening form . As company deals on credit terms I settled all transactions with bank transfers of RTGS or NEFT . In the month of November and December company made unordered billing to me which I objected and asked them to hold on company official email . But they unloaded the stocks by saying that it will be adjusted with return . But after unloading they blackout from their comittment of return of stock . Meanwhile the replacement was also not adjusted in account after repeated requests on e mail . I asked for many times on e mail to settle the account after adjusting replacement and stock return and take the amount if any due towards me . But they have presented my security cheque and have issued a legal notice to give the amount of cheque which is equal to ledger balance