If I understand the question, you have a model initially set up to simulate from time = 0 to time = 10 (for example). However, you stop it at time = 6 to take a look at results. Now, you wish to restart it so that the simulation may continue to time = 10.
Situation 1. You have only "paused" the simulation. Analysis can proceed for the current time step only. Click on "(Re-) run simulator " to restart the simulation from where you left off. The dac file will be appended.
Situation 2. You have stopped the simulation and either (A) selected Exit to Master Menu ... Postprocessor ... and opened the dac file, or (B) closed FEFLOW ... restarted FEFLOW ... Postprocessor ... and opend the dac file. Opening the dac file in the postprocessor allows you to analyze any time step completed by the model. In this case, if you wish to continue the simulation, click on "Continue Simulation". The program opens a new menu from which you can change output options, solver options, and start the simulation. The new simulation results will be appended onto the existing dac file (indeed, it appears that this cannot be changed, if the initial simulation wrote to a particular dac file, so must the continuation).
I have run into situation 2 frequently. For example, if the power goes off during a simulation. To recover, I just open the dac file, and click on "continue simulation". A very nice feature not found in the MODFLOW GUIs! Be carefull however. Stopping and restarting in this way actually writes model results for the last time step completed. This time step will probably not be a time step for which you have specified to save model results (if desired under "Saving time levels at fixed stages as edited").
Situation 3. Your model has finished to t = 10. Upon opening the dac file, you still have the option of continuing the simulation only you must specify a new final time (default appears to by a final time equal to the original file time plus the original model duration, i.e. t = 20 in my example). The results will be appended to the existing dac file (again, it cannot be changed).
I am not clear on what you mean "running it as a batch file" and this may have some bearing on my answers. However, I agree with Chris--Why would you need to merge them (outside of the FEFLOW environment). Strictly speaking, the dac file can be saved as a text-file, and through some careful editing, one could merge two dac files together, but it seems to me that there is an element of fraud involved. The merged dac file may not truely represent a valid simulation.
