[Chin_Lee]

The biggest challenge is not the silicone sticking to glass... it the silicone sticking to acrylic. I am fairly confident your baffles gave away from the silicone and your silicone is still attached to the glass where your baffles were.

Your next challenge is removing the old silicone and cleaning your glass without any impurities between the glass and the next application of silicone.

Pretreating your acrylic edges (that will be siliconed against the edges) with Methyl Ethyl Ketone is your best bet to get the silicone to adhere to acylic. I bought a can of it from Canadian Tire but be very careful using this because it can be absorbed through your skin. It softens the acrylic and allows the silicone to better grab onto the acrylic. I dipped the edges into the the solution (how you do this will your next challenge) for about 1-2 min before applying the silicone.

If I were you, I would:
a) use masking tape on the glass leaving a half inch gap of expose glass where you want the baffles to be installed
b) use a paint brush to paint the Methyl Ethyl Ketone onto 1/2 inch of both sides of the acrylic and keep applying a thin layer for the next few minutes to soften the acrylic surface.
c) Apply the bead of silicone on the glass near the edge of the masking tape where you want the baffles to be placed
d) push the baffle into place from one side
e) finger smooth the one edge where all the silicone have been pushed away.
ensure the silicone is spread onto the half inch edge of acrylic
f) apply another bead of silicone to the other side and finger smooth that side. ensure the silicone is spread onto the half inch edge of acrylic

let it cure

I've seen posts on RC by other people using this method and the silicone to acrylic bond was so strong they were unable to pull the baffles off after the fact.