Any other winbuilder project will do the same thing when cleaning the target directory for a new build.
Well, then EzPE3 is as dangerous as any other Winbuilder project (not more, not less).
Maybe, just maybe EzPE3 could distinguish itself from other projects by implementing further warnings for new users (which basically are the intended audience of something with Ez in the name). .
Most probably a large part of the backup files can be recovered/undeleted.
If you cannot re-run a new backup and you need some assistance for attempting the recovery of the salvageable data start a new thread, to get some assistance.
FIles that were just deleted (but not overwritten) are usually 100% recoverable.