This is one of those situations where a good ORM can simplify things greatly. For example, with EF Core you can add a global filter which will filter out soft-deleted rows in all queries automatically (unless you add .IgnoreQueryFilters()).

It couples nicely with some hackery which turns removes into soft-deletes. You can remove objects as usual and they get soft-deleted in the database.

I've used this in a few projects and it's fantastic.

https://docs.microsoft.com/en-us/ef/core/querying/filters

https://www.thereformedprogrammer.net/ef-core-in-depth-soft-...