Disjunct mode is selected by "Disjunct" checkbox in EDRW's main dialog.
EDRW normally builds a "do not revisit" list of each section rebuilt. For example, after rebuilding segments 3 to 5, EDRW by default adds the range 3 - 5 to the "do not revisit" list. EDRW won't attempt to rebuild the same range again until the score improves by a certain amount or no more sections are available to rebuild.
Settings in the more options dialog control the "do not revisit" list. If the "do not do things twice" checkbox is checked, EDRW keeps a "do not revisit" list. The "cleargain" slider is used to specify the gain necessary to clear the "do not revisit" list.
Disjunct mode is a more restrictive version of the "do not revisit" list. In disjunct mode, after rebuilding segments 3 to 5, each of these segments is added to the disjunct list. EDRW won't rebuild any range containing these segments until there are no more ranges of a given length left or the score improves by a certain amount. Again, the "cleargain" slider in the more options dialog is used to determine when the disjunct list is cleared.
Without disjunct mode, after rebuilding segments 3 to 5, EDRW might still rebuild segments 2 to 4 or segments 4 to 6. In disjunct mode, EDRW would not try to rebuild 2 - 4 or 4 - 6.