How to Work Two Linear Actuator Synchronously by Using Arduino and VNH5019 Motor Driver?
It sounds like you need to watch both encoder outputs and don't let one get ahead of the other. Naturally, they won't sync exactly (i.e., pulse simultaneously) but you can set a limit on how many counts to let them differ by, before pausing the faster actuator while the slower one catches up.

If you need to save positions across a power failure, you'll need to 1) provide enough backup power to keep the system alive past the supply failure to give you time to stop both actuators and store both of their positions in EEPROM; and 2) provide a signal to the Arduino that the supplied power (not the backup) is going down, so it can begin its orderly shutdown.