Product: Bank account or service

I wrote a check for {$170.00} that was presented for payment on XXXX/XXXX/16. I do n't typically write checks but this company was not able to take a cash payment. I only had my checking line of credit check with me at that time. My regular checking account and checking line of credit both share the same account number and I was told upon opening the Checking Line of Credit that the accounts were interchangeable. On XXXX/XXXX/16 my checking account had an available balance of {$200.00}. On XXXX/XXXX/16 I received an email from Navy Federal that I had a returned item for {$170.00} and a {$29.00} fee would also be assessed. I called customer service immediately after I researched my account history and could n't figure out why the check was not honored since the money was available. The first representative I spoke with spent about 15 minutes also trying to figure out why the check was not paid. She then contacted the checking/savings operations department who informed her that my check was not honored because my checking line of credit only had an available balance of {$15.00}. I then explained to her that I used the check with an understanding that both accounts were linked and shared the same account number. She was unable to resolve the issue at this level and I requested to escalate my concern and speak with a supervisor. The supervisor I spoke with " XXXX '' repeated what the previous representative had already said, however I attempted to explain the miscommunication and misunderstanding of the checking account and checking line of credit. XXXX then informed me that I can only use the Checking Line of credit to cover shortages in the regular checking but not the reverse. I then asked if there were any other resolutions because It was definitely a miscommunication and I would be receiving fees from the other company in addition to theirs if they did n't honor the check. I was told there was absolutely nothing else that could be done because it was automatically processed by a system. I then specifically asked if there was any way to manually/force pay the item and at that point she then told me had I called prior to XXXX they could have helped me and force pay it by transferring the money from checking to checking line of credit. I then asked why this information was n't presented to me in the beginning of the call instead of telling me that there was no possible way to resolve the issue. I did n't understand how this could only be manually done by a certain time of day when it was still pending. I then asked if the company had submitted the check as an ACH would it have gone through and she replied yes. I do not understand how Navy federal can say the accounts are not interchangeable but yet they share the same account number and if was an ACH they would honor it but not a physical check. After the call I transferred the funds to my checking line of credit in the event the company tried to resubmit for payment. I was also told by the first rep that my acct would be notated to reverse the return fee. On XXXX/XXXX/16 I noticed a fee was taken from checking line of credit out of the {$170.00} that I had just transferred over now making the account short if the company tried to take payment again. I called and the representative reviewed the account and reversed the {$29.00} fee and transferred it back to my checking line of credit. I am still however concerned with the way this was handled between XXXX shared accounts with the same exact checking number.