A higher voltage rating is OK but you should match the value unless you fully understand the circuit and know for certain changing it will not cause problems.
"Tantalum for the brave, Solid Aluminium for the wise, Wet Electrolytic for the adventurous"
-David VanHorn
That 5pF 3KV cap sounds like it is the ballast cap in the inverter output circuit for the CCFL. You should not go with higher value, but should go for higher voltage if it will still fit the footprint.
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