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The wp search-replace command allows you to restrict the search-replace to specific tables by listing the table name(s) at the end of the command line. Wildcards should be supported. When I use terminus to execute a search-replace command, no matter what table name(s) I specify, I get an error saying "Couldn't find any tables matching:" whatever table(s) I specified. The command fails whether I specify a wildcard pattern or a specific table name.
I discovered this while attempting to update url's in just one (sub)site of a subdomain multisite. I don't know if it's also an issue in a single site (vs a multisite). I thought it might be an issue in Terminus 3, so I upgraded to 4.0.1, but it doesn't work in that version either.