Open Question: Flexible Spending Account Dispute?

Is there a problem depositing a FLexible Spending Account check if I am going to fight for full reimbursement? When I was laid off I submitted $720 valid claims to Paychex, my former employers flexible spending account manager. They said they would pay me back all $720 if they employer would send them a letter. I foung months with the employer who only sent back $355. I want the balance! If I cash the check for $355 does that imply I am throwing away the rest?