Because a few users reported the Build Database dialog's "Indexed Folders" list and the "Excluded Folders" list could be damaged.
When you install 5.06, Hoster opens your HosterInfo.ini file, and copy the "Indexed" list into a new separate file (see the manual for the filename) and the "Excluded" list to a new second file. This insures the two will not interact again.
Thus, 5.06 should prevent your "Indexed" list from disappearing.
Let us know if you upgrade to 5.06 and still have this problem.