Sorry to say, I know of no easy way around this for my particular setup.
However, seeing that you use a TC Electronic BG250 amp, I may a have a suggestion:
To my knowledge, the BG250 does not have EFFECT RETURN nor POWER AMP IN jacks, therefore I will assume you input via the main instrument jack and set a neutral EQ on the amp. With this said, the EQ section on the BG250 perhaps can be used as a single-point, global EQ for all B3 patches. Example, you perhaps could cut BASS on simply the BG250 to compensate for a boomy room and leave all patch EQs as they currently are.
Cheers!
I run my B3 into an ART ProChannel then into my poweramp. The idea is that the B3 gets me into the right tonal ballpark for each song in the set, so I've paid attention to making sure each patch tone and volume is right in the rehearsal room with the ART EQ set flat.
Then, the ART has a really flexible four band EQ, with parametric low and high mids, that is more than a match for any room that I've had to deal with, so i just tweak this as global EQ so that the sound in the venue is roughly the same as our rehearsal space and the job is done. The ART also takes care of gain matching and driving my poweramp.
PS: I've only had one gig where this didn't work really well, this was our last gig on Friday where we only had 10 minutes set up time to figure out how to cope with a big echoey sports hall...I tried and failed, suffering a miserable tone thereafter, but I'm sure that this was just a deficiency of time rather than equipment
If you are running a Pre amp or a or a conventional amp and cab set up after the B3 it really is easiest to use these to globally tune your rig for the acoustics of the room.
However, not everyone is doing that. Whether I am using my B3 or my VT Bass deluxe, I usually run a Boss GEB-7 pedal equalizer after the 1/4 out of the B3 or VTBD which allows my to globally dial in my tone/ acoustics on stage. The xlr goes to the desk, and he can Eq the FOH.
As long as you have set up your patches to sound good in a fairly normal room, a little global eqing should be enough.
Just my $0.02 worth...
Thanks for the replies, guys !
Yes, indeed, the bg250 has only one input (before the preamp - which is very transparent) so I should use its eq.
It was just a little bit counter intuitive to me as I already use the B3 as preamp, so with eq settings.
As for the GEB-7, I was afraid to use too much eq.
Before the B3 I was using a VT Bass (not the Deluxe version) with a drive in front of it, so I was sticked to two settings for a whole show and just had to do a simple eq adjustement due to the room on the 2 stompboxes.
Today my patches are coherent on the B3, I mean, as Jools4001 says, that I set them to have the good output volumes and the good tonal differences when played in the same room.
And, as I understand the problem I encountered, it may be mostly due because of a to high pourcentage of cab sims in my patches.
It seems like the cab sims can work well on a not too much coloured amp as the BG250 in many cases but not all.
So I will rebuild my patches without any cab sims and use my amp eq to fit the rooms (and bring an eq pedal in my gigbag, just in case

).
My goal with the B3 and the BG250 is to travel light and have amost nothing to plug before playing (I like to say to the others : "Hey guys, I'm ready. I'm waiting for you

").
No kidding, I'd like to be able to use the B3 by itself, without other pedals, or I know myself, I will add other stomboxes and I will finish with a big pedal board, using the B3 just as a tuner.