Dear Jayashankar.Prasad,
You have paid the security deposit in wrong account and therefore your application is rejected.
You need to get your mistake rectified. Until the time labour department does not get required payment(s) from you in respective account, no licence will be issued to you and you will be treated as defaulter.
You have to apply to the respective officer DDO i.e. Drawing and Disbursing Officer for rectification of your mistake and request him to divert the amount in correct account.
If you have paid later-on in correct account to get your licence approved and now you wants to collect the amount paid earlier wrongly, then also you have to approch the DDO. Getting refund from DDO, you have to approach the respective DDO.
Telangana rules / regulations and that too for such unique issue with DDO, I feel there is no guarantee that you will get response over here better than this.