It looks like you are running into is a limitation of how Word handles multilevel list definitions. Word is remembering that a particular list level is associated with numbering, so when you return to that level, it tends to reuse the previous numbering format. When you select a portion of the list and change the list type, Word may be modifying the underlying multilevel list definition rather than simply changing those individual paragraphs.
The simplest fix would be to stop using the same multilevel list definition for both purposes. Think of the indentation level and the numbering/bullet format as two separate things. You can have a multilevel bullet list for your normal textbook notes, and when you need a numbered list, create a separate numbered list rather than changing the existing multilevel list level from bullets to numbers.
For example, if your normal structure is Topic → bullet → sub-bullet, leave that multilevel list alone. When you reach a point where you want "1., 2., 3." within the same indentation level, select those paragraphs and use Word's normal Numbering button on the Home ribbon rather than changing the multilevel-list definition. That creates a numbered-list sequence for those paragraphs without redefining the bullet level used elsewhere in the document.
Note that "Numbering" and "Multilevel List" are not the same thing in Word. If you use the Multilevel List menu to turn your existing level into numbers, you are effectively telling Word that this level of that list definition should be numbered. If you instead apply ordinary Numbering to the selected paragraphs, you are changing those paragraphs' list formatting without changing what your existing multilevel bullet level means.
You can also use the "Continue Numbering" and "Restart at 1" commands when needed. So, for example, you could have a numbered list at one point in your notes, return to your normal bullet hierarchy, and later create another independent numbered list. The numbered lists do not need to become part of your primary multilevel bullet structure.
If you want the cleanest setup for textbook notes, I would recommend using Word Styles rather than trying to make one multilevel list do everything. You could have a style for your main topic, a bullet-note style, a sub-bullet style, and a separate numbered-list style. Then the indentation can remain consistent while the numbering type is independent. This avoids the "Word remembers that Level 2 is numbered" problem you are seeing.
In your specific example, I would not try to convert the second list's "1." and "2." back to bullets by clicking the multilevel-list button. Instead, select only those paragraphs and click the ordinary Bullets button. If Word still changes the other list as well, that confirms that both groups are attached to the same multilevel-list definition. The fix would be to separate the numbered section from that definition rather than repeatedly changing the definition back and forth.
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hth
Marcin