I don't have the BR1600 but I'm looking at a manual I downloaded a while back from the BOSS site (
BOSS U.S. - Product Manuals). This may be a different version than what you have so this may not apply in your case.
Under the heading "Loop Effects" (i.e. send - return effects loop) page 112 it states:
"Even if you record an input source to which a loop effect has
been applied, only the direct sound (i.e., without the effect)
will actually be recorded on the track. After recording an
input source, however, the setting for its loop-effect send
level will be automatically copied to the loop-effect send
level of the recorded track. As a result, when the track is
played back, it will sound exactly the same as the input
source with the loop effect applied."
So it seems that the effect "setting" is applied to the track but not the effect. If I understand this correctly, you should be able to go in and change or remove the effect after recording the track