Remove Setup Bootstrap folder on SQL Server 2008 to free space
Solution 1:
According to this site, you shouldn't. You can compress it and remove log files, but you shouldn't delete it.
If I hadn't googled for it I would probably have tried searching to see if any of the files were open, and if not, then copied them to a new location for storage until I was certain the server worked well without it, and if there was an issue recopy them over.
Then again I also have been known to delete the hidden/compressed update files in the Windows directory which is also considered bad practice from what some have said and have had no horrible side effects while freeing up hundreds of meg in space.
An alternative would be to look into installing larger drives and expanding your disk partitions. Depending on the role of the server this could be a major project, though, but in the end if you're in need of freeing space on a database server it's probably time to look at upgrading that subsystem, at least.
Solution 2:
An alternative solution if you're low on disk space, would be to move the contents to a new directory on a different drive/partition, then use mklink /j to create a junction. More info on junctions can be found here https://msdn.microsoft.com/en-us/library/windows/desktop/aa365006(v=vs.85).aspx