If you charge VAT then you are obliged to remit it to Revenue (this applies even if you aren't actually VAT registered). The fact that you realise at some stage that you need not have registered due to low turnover is neither here nor there; since you have added VAT onto the cost of your service, it is not your money to reclaim. If anything, if you shouldn't have been charging them VAT, it is the customers who should get the VAT back (this is a concept known as unjust enrichment).
In the case you've described you can simply cease your registration for VAT from a particular date, on the basis that your turnover will not exceed the threshold. You will not charge / reclaim any VAT from that date on.
However, if you have claimed VAT back on purchase of equipment etc. you will be required to repay a portion of this VAT, as you are no longer going to be using these inputs for a VATable business...
Clear as mud...?!