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London Fixed Gear and Single-Speed is a community of fixed gear and single-speed cyclists.
iamalex
Bobbo
This would traditionally be done with burnt sand and linseed oil mastic. I wouldn't use silicone because you risk trapping moisture behind the silicone which will lead to rot issues. Lime putty would be good in this situation as it's breathable so any trapped moisture will be able to escape.
That soft spot could be the tip of the iceberg. It needs chopping out and treating / filling with timbabuild or repaircare.