Difference - Batch Training or training multiple times?
There will not be any difference between :


Training all batches + Epoch in one go 
Saving a checkpoint and resuming the training later 


Saving a checkpoint is a very good practice. It is not uncommon for training to fail due to environmental issues (E.g.: Spot instance on AWS gets kicked out , PC crash). 

With Libraries like Keras, it is very straight-forward to checkpoint models.