will messed up 02 sensor affect a custom flash?

It depends on what paramiters the flash uses. Your VCM might have the O2 overide. Read the tread on (tuning for dummies) it helped me start off.
Ask who is doin the flash about the O2. Best if you change it and put an upgraded unit thers a tread on that as well.

if it's either B1S1 or B2S1 then yeah it can really effect your overall performance. The S2 sensors are there just to measure catalytic efficiency for emissions, but the S1's are what the computer gets your a/f ratio from. If you think it's messed up you can goto autozone or oreilly's and get an OEM replacement.