Quote Originally Posted by The Vicious Monkey
There might be changes to the regular files besides those in the EB folder.
No, there are no EB files in the vanilla structure anymore thanks to DolGuldur, apart from the icon and an RTF document with some information at the RTW root. Still you might break EB by installing another mod in the same RTW. Keeping EB in an own, otherwise clean, 1.5 RTW is the safest way.

EB installed files in the vanilla structure in all previous versions.