The Igros Moshe (Orach Chaim 6:13) asks your question on Rashi, as well as a number of other questions. He concludes there that just as a Korban can be redeemed when it has a blemish even though it is Kedushas ha'Guf (and then its sanctity descends to Kedushas Damim), a shul which has fallen into disuse and is d'Rabanan in its sanctity may be sold. The actual sale demonstrates that the shul is no longer needed for its purpose and -- just like the Korban with a blemish -- it can be sold.

Rav Moshe zt'l adds that if it is being sold because they need another shul in its place, the Kedushah remains on the money, and if it is being sold for the money this reveals that they do not require a shul. However, this is all if it is sold with the consent of the entire city and its representatives, since -- if they have not agreed together to sell -- there may be some people who still want to use it as a shul. For this reason, when it is sold the Kedushah stays on the shul and the money even if they sold it for the money.

However, if the entire congregation agrees to sell and wants the money, this demonstrates that it has no purpose whatsoever and therefore it can be sold for profane purposes, and the money can be used for other purposes, but if they need another shul the Kedushah remains on the money. In the case of 26a, since it is not with the consent of everyone, the Kedushas ha'Guf remains and both items have Kedushah, but on 26b the Kedushah is transferred to the money (since this is accepted by the entire city) and will be used for the other shul. (They needed to sell the shul for whatever reason; perhaps the city did not allow them to continue prayers there, etc.).

Yoel Domb