Updating an indexed column performance impact in SQL server
Modifying the value of a field used in an index will certainly take more time than modifying the value of a field not involved in an index.  Having said that, the WHERE clause in your UPDATE statement could be used to speed the search for matching rows when the field in question is part of an index.  In this example, where you have a boolean field present in 100 million rows means the selectivity of the field is so poor that a table scan will likely be required anyway.  I would estimate that updating this particular field would be quicker if there was no index on it.

However, to answer your question of whether or not there will be performance impact on your system is really only answerable by you since there are a many other variables to consider such as storage speed, RAM availability, etc.