The problem I ran into with regenerating the obstacle map is that it is not optimized for moving objects. So it chugs through everything, even objects that have been in the same place forever, and it causes a little pause in your game that's noticeable.
However, placing such objects outside of the layout may just work like Arima said. It's worth a shot.
The only real issue I see even with using a properly optimized obstacle map is that your enemies will consistently move in odd directions to avoid each other while moving, or not move at all.
So you would need to make them move only a bit at a time.
For instance, say you have two enemies, one behind another in a back alley, with only room wide enough for one enemy.
If they both use pathfinding to get to the player, both set to avoid colliding with other enemies, the one closest to the player will continue to move towards the player as expected, however, the one behind the enemy is now blocked from access to his destination, and will not move.
It's extremely tricky in C2. I had to abandon one project for now because I simply don't have the experience in pathfinding enough to overcome these obstacles, and because the pathfinding plugin isn't quite up to par when you have any dynamic obstacles.