Reread original posts last evening. Had not noticed thie silicon in-hull business as I was concentrating on the symptoms which resembled my problem exactly...
You need to get the transducer out of the silicon and into either mineral oil or epoxy for it to work properly inside hull. Once you get the silicon problem out of the way you can start working on troubleshooting your depth sounder.
Now I would think that epoxy would be downright stupid at this point since it is more or less permanent and we do not know if the unit is working. If it were working than epoxy is not a bad idea if you get the bubbles out. I would suggest testing with mineral oil or even water ... and maybe even while tied up just hang the transducer over the side to test for accuracy.
What should you do???
Haul the boat and mount the transducer properly! This is a thru-hull transducer and is meant to be mounted that way. You would bed the transducer with something like 3M 5200 or even 4200 if mounted thru hull. Most people would suggest 4200 since 5200 is semi-permanent.
If then your sounder is still working as you suggest you will have the identical problem to the one I had. That problem was fixed by replacing the display unit.
Best of luck
PS. As annoying and expensive as a one day haulout is it is usually best to do this sort of thing the right way to save yourself months or years of frustration ....