LPWANs are a class of technologies that have very low power consumption and high range of communication. Along with its various advantages, these technologies also have many limitations, such as low bandwidth, connectionless transmission and low processing power, which has challenged encryption methods in this technologies. One of the most important of these challenges is encryption. The very small size of the message and the possibility of packet loss without the gateway or device awareness, make any of the cipher chaining methods such as CBC, OFB or CTC impossible in LPWANs, because either they assume a connection oriented media or consume part of the payload for sending counter or HMAC. In this paper, we propose a new way to re-synchronize the key between sender and receiver in the event of a packet being lost that will enable us to perform cipher chaining encryption in LPWAN limitation. The paper provides two encryption synchronization methods for LPWANs. The first method can be synchronized in a similar behavior as the proof of work in the block chain. The second proposed method is able to synchronize the sender and receiver with the least possible used space of the message payload. The proposed method is able to synchronize the parties without using the payload. The proposed method is implemented in the Sigfox platform and then simulated in a sample application. The simulation results show that the proposed method is acceptable in environments where the probability of missing several consecutive packets is low.