There was a bugged version of the REX installer, that removed every other 3rd party module from the DLL.XML file so, all our sceneries (and every other 3rd party product requiring addons modules) stopped to work, but I think this was fixed a while ago. Check your version is the fixed one, because nobody else reported this problem since it was fixed by REX.
Can't think of any reason why UTX should create issues to the scenery but, if you say this is fixed by reinstalling ENBR, it's maybe another similar issue with corrupting your DLL.XML or EXE.XML files, which are fixed back by running our installer.
In both cases, since it's fixed by running our installer, it really seems something caused by those products but, apart for the initial issue with the bugged REX installer, nobody else reported this.