Is it permissible for me to obtain invoices through another method to cover the deficit after an accountant took the invoices from me and did not give the money to the shop owner, and do I owe expiation if I am unsure about the oath I took not to do such a thing again?

If you bought items for your workplace and submitted the invoices to the accountant, and they were lost, and the payment was not made, then you were asked to account for them, and you were forced to create fake invoices to prove your work and avoid being obligated to pay, then if this does not lead to the loss of your workplace's rights and you found no other means, there is no harm in that.

As for the oath, as long as you doubt whether you actually swore an oath or not, there is nothing upon you, because the original state is freedom from liability and certainty is not removed by doubt.