It seems that altera has two remediies for their old warning:
1) an almost_empty flag
2) protection circuitry(extra logic)
This what they say(dc fifo user guide)
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Underflow and overflow circuitry protections are enabled by default to prevent FIFO data corruption. Turning on the option from the FIFO
MegaWizard plug-in disables the protection circuitry.
When the protection circuitry is disabled, writing to a full FIFO can corrupt the FIFO dataand reading from an empty FIFO can return unknown data and produce unpredictable future results; however, when the protection circuitry is disabled, the FIFO megafunction uses fewer device resources.
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