If all you are looking for is matching keys between the two queries, then this should work:
SELECT
ClaimId,
LineNum,
EncounterLineNum,
EncounterType,
InternalICN
FROM IntEncTracking.EncounterList el
WHERE e1.bypassflag = 1
INTERSECT
SELECT
ClaimId,
LineNum,
EncounterLineNum,
EncounterType,
InternalICN
FROM IntEncTracking.EncounterList el
WHERE e1.bypassflag = 0
For fast, accurate and documented assistance in answering your questions, please read this article.
Understanding and using APPLY, (I) and (II) Paul White
Hidden RBAR: Triangular Joins / The "Numbers" or "Tally" Table: What it is and how it replaces a loop Jeff Moden