In my experience, whether or not the stripper effects filler or glued in bits of wood depends on the stripper. "Aircraft" stripper (the strong stuff with MEK, etc.) will soften filler. Lesser strippers, like the Citri-strip you plan to use, are much more gentle, and can be carefully used without turning the filler into a gooey mess. YMMV, and all that.
I don't understand why you hesitate to sand the existing finish off. If you sand it to the wood surface, you'll be starting at the same place you will be if you strip down to the wood surface...?
Randall
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