Replacement of Transformer

I am afraid the fault levels of 10kV bus will go up considering that the two generators are now paralleled at 10kV bus before taken to the transformer 10kV terminals.

It may also increase the fault current contribution to 11kV bus from generators but this may not be much of a concern.

...after all, <...we...> seems to suggest that there is one...

As Raghun explains, the fault current will increase considerably at your generator breaker. A three winding transformer is a common way to limit fault current between two high fault current sources, especially with local generation. The contribution from one generator has to pass through 2 reactances to get to the other generator breaker. As a guess, you need 1000MVA switchgear for your breakers. The decision to replace the transformer with a different type is likely a mistake that could result in an explosion or fire if both generators are on line and one of the breakers is commanded open by fault relaying.

The likely economical fix for this mistake is to purchase and install a pair of series reactors between each breaker and the transformer, restoring the missing impedance provided by the original transformer winding configuration.

When you consult an actual electrical engineer to size the reactors, you should confirm the actual fault duty of the generator breakers, based on current data, including the subtransient reactance of the generators.