It depends a bit on where your EGPWS is getting its position information and is it "enabled". In the Honeywell and R-C systems I fly, if you leave the GPS enabled, the EGPWS should work fine, if the airport in the database and the DB is up-to-date, regardless of QFE or QNH. The EGPWS works off of GPS and WGS-84 which is the datum that the DB elevation and obstacle information is formatted.
However, you cannot use VNAV or FMS approach in QFE operations due to incompatible altitude information. You must fly approaches in raw data.
If the FMS enters landing elevation for pressurization, it needs to be put in Manual and a manual elevation of Zero entered.
It would be easier if we could enter "0" in the FMS landing elevation, all would be well.
You must turn off TERRAIN, if you have disabled the GPS receivers, btw. Because the EGPWS has no GPS positional information to work with.
GF