[Kolde]

Considering while the two books they come from are similar they do have some different PrCs in them I'd say that ones not completely redone in PGtF, are likely still meant to exist as they are, question being was Agent a redo of Scout. There's also this statement in the same book: "While the version 3.5 revisions to the DUNGEONS & DRAGONS game included a number of relatively minor changes and updates to the game system, the majority of your existing 3rd Edition FORGOTTEN REALMS supplements and accessories are still perfectly usable in your game. FORGOTTEN REALMS Campaign Setting: Chapters 1 through 3 of Player’s Guide to Faerûn update and supersede Chapters 1 and 2 of the FORGOTTEN REALMS Campaign Setting. The rest of the Campaign Setting is unchanged by the v.3.5 revisions to the DUNGEONS & DRAGONS game. However, Chapter 7 of this book (the Campaign Journal), offers some updates on major story developments reflected in the Return of the Archwizards and War of the Spider Queen novel series."

Judging by the differences and similarities of the class(es), I'd say that Agent was meant to replace Scout. But they seem to leave it open to the DM whether or not to use both.