personally leaning towards "...the dye / colorant may (have) separate(d)...."
if it's a powder mixing with a liquid, then maybe "...pigment may (have) settle(d) (as in fall out of solution) / separate(d)..."
if it's two liquids, like oil and water, over time and without emulsification they will "separate" into visible and distinct layers.
Slightly OT, try to change the "voice" to active from passive. "... Before using gel, mix gel vigorously with a suitable / an appropriate stirrer as the dye / colorant / pigment may (have) settle(d) or separate(d).
Sounds verbose only because there are so many choices and verb tense to clean up.
Use a suitable / an appropriate stirrer to mix (stir / blend?) the PU-Gel. Pigment may have settled / separated (during storage).