It's pretty obvious that Elizabeth Montgomery/Samantha looks varying levels of pregnant during season 2. Here are the episodes in filming order (rather than broadcast order) that would help explain things. I've heard "The Magic Cabin" was the last episode Elizabeth Montgomery was actually pregnant in and "Maid to Order" was a pillow, but as you can see from the filming schedule, she actually was pregnant up until "My Boss the Teddy Bear."

It's most interesting to see when "Prodigy" was filmed, since it was held back to the end of the season as a tribute to the late Alice Pearce and framed as a flashback. Gladys' role would be filled by Abner's sister "Harriet Kravitz" (Mary Grace Canfield) during Alice's last days ("Follow That Witch" part 1 and 2) and after her passing.

1. #3962 #37 ALIAS DARRIN STEPHENS 5/20/65 9/18/65 (1)
2. #3964 #38 A VERY SPECIAL DELIVERY 5/26/65 9/23/65 (2)
3. #3949 #39 WE'RE IN FOR A BAD SPELL 6/4/65 9/30/65 (3)
8. #3960 #44 A VERY INFORMAL DRESS 6/14/65 11/4/65 (8)
10. #3968 #46 JUNIOR EXECUTIVE 6/18/65 11/18/65 (10)
36. #3961 #74 PRODIGY (Final B&W episode) 6/24/65 6/9/66 (38)
4. #3969 #40 MY GRANDSON, THE WARLOCK 7/l/65 10/7/65 (4)
12. #3972 #48 A STRANGE LITTLE VISITOR 7/8/65 12/2/65 (12)
5. #3975 #41 THE JOKER IS A CARD 7/16/65 10/14/65 (5)
9. #3971 #45 AND THEN I WROTE 7/21/65 11/11/65 (9)
7. #3973 #43 TRICK OR TREAT 7/29/65 10/28/65 (7)
11. #3966 #47 AUNT CLARA'S OLD FLAME 8/4/65 11/25/65 (11)
6. #3965 #42 TAKE TWO ASPIRINS 8/12/65 10/21/65 (6)
15. #3959 #52 THE MAGIC CABIN 8/19/65 12/30/65 (16)
14. #3974 #50 SPEAK THE TRUTH 8/27/65 12/16/65 (14)
#51 VISIONS OF SUGAR PLUMS (RECUT VERSION) 12/23/65 (15)
16. #3978 #53 MAID TO ORDER 9/2/65 1/6/66 (17)
13. #3983 #49 MY BOSS, THE TEDDY BEAR 9/10/65 12/9/65 (13)
Elizabeth Montgomery's son Robert Asher born 10/5/65
17. #3989 #54 AND THEN THERE WERE THREE 12/10/65 1/13/66 (18)
18. #3986 #55 MY BABY, THE TYCOON 12/15/65 1/20/66 (19)
#56 SAMANTHA MEETS THE FOLKS (RECUT) (REPEAT) 1/27/66 (20)
19. #3987 #57 FASTEST GUN ON MADISON AVENUE 12/21/65 2/3/66 (21)
20. #3991 #58 THE DANCING BEAR 12/29/65 2/10/66 (22)
21. #3977 #59 DOUBLE TATE 1/3/66 2/17/66 (23)
22. #3992 #60 SAMANTHA, THE DRESSMAKER 1/10/66 2/24/66 (24)
23. #3984 #61 THE HORSE'S MOUTH 1/17/66 3/3/66 (25)
24. #3985 #62 BABY'S FIRST PARAGRAPH 1/21/66 3/10/66 (26)
27. #3990 #65 DISAPPEARING SAMANTHA 1/27/66 4/7/66 (29)
25. #3996 #63 THE LEPRECHAUN 2/3/66 3/17/66 (27)
26. #3997 #64 DOUBLE SPLIT 2/10/66 3/24/66 (28)
PREEMPTION (PREEMPT) 3/31/66
28. #3995 #66 FOLLOW THAT WITCH (PART 1) 2/17/66 4/14/66 (30)
29. #3999 #67 FOLLOW THAT WITCH (PART 11) 2/22/66 4/21/66 (31)
Alice Pearce dies from cancer 3/3/66
30. #3970 #69 A BUM RAPS 3/8/66 4/28/66 (32)
31. #3967 #68 DIVIDED HE FALLS 3/12/66 5/5/66 (33)
32. #3902 #70 MAN'S BEST FRIEND 3/18/66 5/12/66 (34)
33. #3901 #71 THE CATNAPPER 3/24/66 5/19/66 (35)
34. #3900 #72 WHAT EVERY YOUNG MAN SHOULD KNOW 3/30/66 5/26/66 (36)
35. #3905 #73 GIRL WITH THE GOLDEN NOSE 4/6/66 6/2/66 (37)

The filming schedules are interesting. As is when they get the renewal notice between seasons. I Dream of Jeannie filmed two season 2 color episodes before finishing up filming of the black and white first season. Those were held over until it went to color the next TV season. So in two second year episodes they have the season 1 house set and incidental music (both changed for season 2).

I wonder if they were finishing season 5 just before starting season 6 with little to no break in between. So Sargent had to be found and hired rather quickly.

Dick York's collapse was around January 6, 1969, and Dick Sargent was hired in late January. They kept right on filming, possibly due to Montgomery's upcoming pregnancy. https://www.sitcomsonline.com/boards/showthread.php?t=272755