From what I have read in the past as long as you are not connected to a VAC server while using SAM you should be okay. I've used it before without issue to reset achievements in games that I wanted to do over again.

To do it you would need to run Steam and be signed in to whatever account you want to manage the achievements for. Then you run SAM and wait for it to load all of the games, which if you have several hundred plus could take a minute or two depending on how fast it is processed. Then once the game list is populated you would double click on the logo for the one you want (on a side note: why doesn't SAM cache these for the next time the program is run for crying out loud, ugh) to open the configuration window for that game, where if I recall correctly there should be a mechanism such a button or checkbox to select all of the achievements and set them as locked. Then you hit a button on the upper right to perform the action and you are done with that particular game and can close the window for it.

edit: If for some reason a game you want to manage doesn't appear in the game list (not sure if games removed from Steam store will show for example) then you can manually 'add' it by putting in the appid # in the search field at the top of the main window.

edit 2: there was no update to the program for years but it looks like it is hosted on github now and someone put out some new versions over the past year. It looks like it still doesn't cache the game logos though. Sigh.