IF ....... you should get some Brett contamination in the lines, as long as the beer doesn't stay in the lines for a long time (we are talking months for a beer with alcohol to be affected by a few cells of Brett), there is no need to worry.
Normal sanitizing should be able to knock the population down to a controllable level. Remember; sanitizing doesn't kill everything, it just takes the potential contaminants down to a level where they should not affect the taste of the beer.
The big concern with Brett is when using it in fermenting vessels and transfer hoses. If a few Brett cells get into a beer from a hose while transferring to a secondary fermenter, it will have time to reproduce and start affecting the beer.