It will work, when working with light colored woods sometimes is I suspect I might have misses a spot of glue I will wet the whole surface with mineral spirits to see any glue spots and I have used Minwax Polyacylic and it came out fine
If you mean you want to clean a finished piece of furniture and use a waterborne finish then that presents a whole bunch of problems. A waterborne won't just adhere to a lot of finishes. It's kind of like the dilemma of painting an oil based enamel with latex paint. It can be done but you have to prime the oil based enamel with an oil based primer. Likewise with the waterborne clear coat, it can be done but you may need to seal the existing finish with Zinsser Sealcoat. The Sealcoat will bond to most finishes and the waterborne clear coat will bond to the Sealcoat.
I used to use mineral spirits before finishing, but found it always left the wood "oily". not a big deal if you are doing an oil based finish, but sometimes my water based finishes would bubble up in spots. I now use el cheapo rubbing alcohol to do final clean, no issue with residue or odor. I use Rustoleum Pro Finisher water based poly for floors for most projects.
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