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Does this mean that percentages are deprecated and won't work on anything anymore?
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Percentages are fine but are calculated based on tag parent size. The vh and vw units are calculated based on the device view box size. Usually a subtle difference but sometimes important.
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I can do a bulk update, but I've got a gazillion epubs
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First, test to see if the unit change solves the problem you complained of — and then figure out the next step.
On my Windows 10 test machine, I found that the unit change did not solve the problem. This involved chapter heading images placed thru the CSS file. The images bled into the next page if the Calibre viewer was not a certain width. Weird effect. If your images were placed more conventionally, Kovid's suggestion might work for you.