hi Diego2011
as far as I know, please anyone can feel free to correct me if I'm totally wrong, your wife's US residency card is not affected by the Paraguayan "repatriación", at least not by the Paraguayan government. However, "repatriación" can only be requested once in your life, normally, at least as far as exemption of custom duty is concerned.
My sister-in-law returned from Germany last year and was able to keep her German residency status.
If your wife decides to make use of her repatriación, then you must make sure to start the process early at the Paraguayan embassy in the USA, because you first need to do some paperwork there before coming to Paraguay. A list of all your household items, better in Spanish + English, must be submitted to be legalised. However, if she fulfills the requirements of repatriation, all of those legalisations are free of charge. Your B/L for the container must also be legalised by the embassy. VERY important! Once here you must visit the "Secretaria de la Repatriación" and be extremely patient with those civil servants. You must also find a good "despachador".
Another thing is, that your wife might have to pay something anyways, because there are some port duties that have nothing to do with customs. But the total of costs is much less than a normal immigrant has to pay.
And believe me, it is worth it! If you have some pieces of furniture that you really like, books, souvenirs, etc., you won't find those again here. Of course you can find everything here, but "everything" has a price and according to my sister-in-law it was worth it to get that container.
I hope this can help you but to make sure, you should contact US officials concerning the residency status. Maybe there is a limit of time allowed to be away from the USA like a few years or so.
Julie