Assuming these are the screw attached. I'd take 'em off clean all that silicon off and reinstall with 3m 4200 or 3m5200 (more forever) . Those products are made for boat applications. I've used 5200 underwater for years.  Put the product under the flange between flange and deck. Screw holes too. On an area where you might one day refinish I'd use 4200. It stays soft. 

The other kind epoxys on. I doubt you used that one. 

The screw on inspection covers will leak sometimes when under water through the threads of the screw on covers but not "flowing". 

   Yeah, I used the one that are attached with screws. Would you still use screws with 3M 4200?

4200, yes.  For a good seal, screw down just until it squeezes out evenly.  After it cures a bit, tighten screws down some more.  With 5200, you might get away without the screws, but they are helpful for getting an even squeeze anyway.

.....Michael

   Thank you! Cleaning off the silicon turned out to be a big nuisance (I am avoiding using sharp tools). Any tips or ticks?

Other than that, I am going to try 4200.

Menwhile, feeling silly that I damaged a perfectly good boat...

   I use a five in one tool. Sharp not too much but effective.