Praise be to Allaah.
If your work and training were done in the Islamic branch
of the commercial bank and you are not certain about whether the bank’s
dealing and transactions were haraam, then there is nothing wrong with
your having taken money, especially since the branch had a shar‘i
committee supervising it.
Similarly, if the bank had started to turn into an Islamic
bank and you yourself did not do any haraam work in it, there is nothing
wrong with your having taken any money, because it is permissible to work in
such a bank.
If it becomes clear to you that this branch was doing
riba-based transactions and that there that was nothing to differentiate it
from a regular commercial bank, and the money you took is still with you,
then you should get rid of it by giving it to the poor and needy or spending
it on other charitable causes.
For more information, please see the answer to question no.
81915
And Allah knows best.