Plugin is way too complex for me to follow code. 🙁
I can say that in practice after emptying minify cache both CSS and JS concatenated files are rebuilt with same name, using same numerical id.
So my educated guess would be that numerical id is tied to file contents, rather than being random or timestamp-ish.
Anyway it is probably best to contact plugin’s developer and get first hand info. He is registered here ( Frederick Townes ), but not very active – so email or official WP forums are better for that.
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