Hi,
It won't be necessarily identical, since you are dealing with LSTM network which means the testing data is sequencial in nature, so if each time step given as input to trained network will not be necessarily give same output as compared to giving all seqeunces at one time because of LSTM behaviour. The second approach which you tried will consider each time stamp as independent identity while the first approach where each time stamp is connected to previous timestamp. If its a general CNN network then sure both the result will be identical.
I hope my explaination make sense.
Cheers.