Ah - the charging circuit is usually equipped with thermal protection, so that if it gets into a dangerous condition, it stops charging.
I never drained the batteries while using mine, but it never took more than a day to recharge completely to the point that the UPS' charger would stop outputting voltage.
Of course, the idea of a UPS isn't to allow you to keep working, it's to provide you with a surge buffer and keep your machines running (hopefully) until the power comes back online, or until you can get a real backup system running, or to provide you enough time to finish what you were doing, and shut down/turn off safely.
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