Let me clarify. If all these employees were selected at a common examination and their educational documents were collected at the same time as a part of the common exercise, it may be the SAME cause of action where only one offence is possible. On the other hand, if they were selected in different examinations or different selection processes or at entirely different times, in that case the cause of action would be different (though in this case also, you can try to convince the court that the collection of documents is done under the SAME rule or order, hence a common cause of action).
However, you have also stated that the employees have joined over a perod of two years. As I mentioned earlier, Section 219 is applicable for offences committed within a space of 12 months. So, this may be another impediment to have a single trial.
But, let me raise another basic issue. From the descripttion given by you (though one has to see the FIR, Chargesheet and other relevant papers to get a full idea of the case), I doubt how an offence under Section 406 IPC can be made out. There are 3 basic ingredients of the offence under Section 406 IPC:
(1) Accused must have dominion over property or must have been entrusted with property (this apepars to be satisfied here).
(2) He must dishonestly misappropriate the same or convert it for his own use, etc. (it apepars that this ingredient is not satisfied).
(3) Such misappropriation or conversion must be in violation of any direction of law, or of any legal contract, etc., prescribing the mode in which such trust is to be discharged (in the absence of full knowlege of the case papers, I cannot say whether this ingredient is satisfied, though it appears from your descripttion that this ingredient is also not satisfied).
Therefore, it appears doubtful whether an offence under Section 406 IPC is made out in these circumstances. Of course, a civil action can be taken in this situation, but an offence is doubtful. A definitive opinion can be given by a person who has seen all case papers.