When you import a schedule CSV into a page that already has sessions, every People IDs column in your file replaces the contents of the list it points at. That's what lets you keep your lists up to date from a spreadsheet — and it's also how a re-import can empty a list you didn't mean to touch.
What each column does:
A cell lists everyone who should be in that list. Anyone left out of the cell is removed from the list.
An empty cell removes that list from the session.
If a column isn't in your file at all, that list is left as it is.
So if you only want to change some of your lists, leave the other columns out of the file rather than including them with blank cells. A column you leave out is safe; a column you include with nothing in it empties the list.
The same goes for a column you include but don't map: if no field is chosen for it in Map your Fields, the import ignores it and leaves that list alone.
Nobody is deleted from your app by a re-import. People taken off a list stay on your People pages and on any other sessions they're attached to.
Related articles that might be helpful:
Start with the guide to lists on schedule items
See how you can import people into named lists from a CSV