anybody run into this

I was removing the mouldings around my windshield and rear window.
When I was removing it around the windshield I was having a heck of a time getting the moulding tool to catch on the clips.

I finally got one off with out messing it up. I found out why I was having trouble.

The windshield must have been replaced at one time and in the channel between the body and gasket someone had filled it with a black mastic material. It was keeping the tool from contacting the clips easily.

I don't think this is the proper way or is it.

The rear window didn't have any around it.
I thought I ask because a lot of you have removed the windshields when doing body work.

Here's a few pics and a little diagram.
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Thank for any info!