Vertical Justification - Resetting to Align Top when changing copy

Paragraph styles such as a heading don't have vertical alignment settings. That's a function of the text frame it's in. (That you have headings in a separate text frame may be an issue; that's not particularly good working practice. But I'll assume you have your reasons.)

What you need to do is set an Object Style for these heading frames, with Align: Bottom being the key setting. Apply this style to all heading frames and you should never see this changing behavior again.

Sort of a side note, but: you may have changed an app default without realizing it, and that setting is reasserting itself each time.

If you change a setting with no object (text, frame, graphic) selected, that setting becomes the new default. Click on the pasteboard or somewhere in the UI so that nothing in the doc is selected, then click on a font, color, stroke, effect etc. It will become the default setting for everything you do after that point.

Always make sure all relevant styles (Paragraph, Character and Object) are fully defined and don't have an override flag (+). That will cure a lot of "changing" behavior like you're seeing.