I'm not sure I understand your question so I'll first share my understanding of your issue: Are you saying that you stored some old counters to make room for the newly purchased counter to complete Goal 4, then closed your app and went to sleep yet when you woke up this morning, the old counters were back on the board and the new counter was not there?
If the above is correct, then it just sounds like your game rolled back and didn't sync with the s8 servers before you closed your app for the night. Lots of players experience this issue in nearly every s8 game and over time have found visiting another bakery or writing on their wall to 'force' a sync will help stop the rollbacks. Other than forcing the sync, there's not really anything else we can do about random rollbacks, to my knowledge.
The payment method you have on file with the app store should not be connected to or effect the app itself in any way. I can't really think of any reason to share that info with s8 unless you're disputing a charge on the account.