First, when you make a change to a profile you need to update all your recipes with the old profile one at a time. BeerSmith treats all recipes as a self-contained archive so that if you change a profile later on it will not be reflected in recipes that have already been brewed.
Now, even if you updated the equipment profile in your recipes you will get the same results you had before. The reason for this is that there are two different material balances that the program is trying to solve. The first is the volumes throughout the process. When you changed your mash tun dead space figure, it adjusted the amount of water you needed to mash with to compensate for this change.
The second is the sugars from the mash. BeerSmith relies on the brew house efficiency value you supply in your equipment profile to calculate how much sugar is needed from your grains. It takes your brew house efficiency and the volume into the fermenter to figure out the amount of sugar it needs. It then adds the sugar lost in each of the volume losses specified in the equipment profile, adjusts for the boil off rate, and sets that total amount of sugar it requires from the mash. It reflects this by changing the mash efficiency to draw the same amount of sugar you needed at the end of the process, taking into account the various losses throughout the process.
So for instance, if you set up for a 75% efficiency with a 5 gallon batch the program will calculate that 75% of the available sugar in the grains (based upon the grain potential) will make it into the fermenter. If you had no losses in the system, the calculation would assume a 75% mash efficiency. Now, if you added a gallon of losses into the equipment profile without a change in the brew house efficiency or a change in the grain bill, the program will calculate that you needed an additional 1 gallon of wort at the 75% efficiency and adjust the mash efficiency upward to draw that amount of sugars from the mash.
When you make a change to the equipment profile for a change in the volume of process losses, you need to adjust the brew house efficiency to bring the actual mash efficiency into alignment with the previous figure from before you made the change.