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If I click skip updates, will those updates still be applied the next time I choose to update, or will they be skipped completely and lost forever?

Quote:will those updates still be applied the next time I choose to update

^this

Nothing really will happen,even if you skill a year of updates,updating it will download the latest version with everything applied

It just saves you the hassle of:
1.Going to this page
https://github.com/PCSX2/pcsx2/releases
2.Download the latest version
3.Extracting it into your pcsx2 folder