Not usual to only get 3 hits when searching on Google nowadays but one of these were:
which at a first glanze seems to fit the description.
A workaround mentioned (would probably need adjustment for VyOS) is to use:
zebra nexthop-group keep 1
Question: Do you have ECMP configured? Do you get the same error with ECMP disabled?
According to above link there seems to be a racecondition between Zebra (FRR) and the kernel when ECMP is being used and one of the participating interfaces bounces which results in the routes being lost.