How long will peanut butter and raspberry jam thumbprint cookies last?

Sorry for typo: I meant fill them now. Thanks.

No food safety concerns with cookies in general; nothing to 'go bad' as they have high sugar content (sugar and salt are both preservatives)and have been baked. If they had raw egg, that would be cause for concern, but they don't! It is true that nuts and nut oils can 'go rancid' if exposed to a long period of sunlight or hot storage conditions, but that is probably irrelevant for your cookies. Refrigerated in a tightly sealed container is the best way to store them, imo; adding the jam now won't adversely affect them.