I think the arduino can't receive data when interrupts are disabled
So will the sender wait until serial can receive bytes again
The sender has no idea that the receiver is ignoring serial data.
or are the packets lost?
I'm using a leonardo with FTDI connected to pin 0 and 1.
Makes no difference.
You will probably need to implement some sort of handshaking between the sender and the receiver, so the sender know when it is safe to send.
Keep in mind that serial data reception (and sending) is not the only thing impacted by disabling interrupts. The clock can't tick, either. That is, millis() doesn't increment.