If you just want to seal the grooves, silicone will work. It is very flexible and does not dry hard. I have used it for house projects. IMO It would be better to use a real 2 part epoxy that hardens and then you would have to sand it smooth. It would be hard as a rock. That will help to keep the neck straight.
Silicone will NOT work!!
Do NOT use it. You will ruin the fretboard, guaranteed.
It is flexible and compressible - you MUST fill the grooves with a substance which does not compress and is not flexible. Otherwise you're taking away the structural integrity of the fretboard by cutting grooves across it! The result can be that the neck will bow forward and cannot be corrected.
The most common options for inserting material into those fretlines are either thin slices of hardwood, or plastic styrene strips available at craft stores. Both are hard material which will not compress. If you use the correct type of epoxy and fill the cracks with it, you can achieve the same thing since epoxy is not compressible once cured.
There are different kinds of epoxy, and you need to do research on which type to use. if you get the wrong type, or if you are slightly off on mixing the epoxy, you will end up with a sticky mess which may never cure - meaning the neck is useless.
This is a project which should only be attempted after spending a few days doing research on options and technique, and searching the web for information. Epoxy is a difficult material to get right, and using it is definitely a higher degree of difficulty!
If you skip the epoxy, it's relatively easy to de-fret a neck and fill the lines with hardwood or styrene glued in place with super glue, then carefully trim the excess material and sand VERY lightly, achieving a nice finish to the fretboard. Estimate about 5-10 hours for a nice job.
This bass was defretted and white styrene was used to fill the fret lines so that the lines would still be visible. A single coat of Tung oil was applied to the fretboard after light sanding. I can run a finger up and down the neck and not feel a single fretline.
My recommendation - you're getting into something deeper than you realize. If you MUST de-fret, get Dan Erlewine's book on guitar repair, study the info you can find on the web, and forget the epoxy.
