Why the "but"? You didn't ask that question.
Ok... I'll take a look.
Irf540 - this I larger and has a higher gate charge. If switching speed is important, it may not be a good choice. Also the turn on turn off times are significantly different. If the ratio of one to the other is important, this may be a poor choice.
Irfbc40: This has a far higher Rds(on) which may make it unsuitable if voltage drop or power dissipation is an issue. This is in addition to the higher gate charge (with the same arguments as above). The continuous drain current is lower -- a problem if current is high. Similar issues with turn on and off times and delays as above.
As to whether they are a suitable replacement, I would need to know far more about how they are being used.