How would I use Linux as a central, secure gathering point for Windows shares?
I am not confident that my interpretation of the question is correct. Perhaps you could provide a little more information if my answer does not seem to cover your needs.
Samba provides a facility known as MSDFS (Microsoft Distributed File System) that allows centralized access to resources that reside on multiple CIFS servers. Samba will simply redirect access to the target host/s.
So, that is one way that a Linux server can act as a central "gathering point" for distributed data that resides on MS Windows shares (CIFS resources). The neat thing about MSDFS support in Samba is that this facility allows the site to move data between servers without disruption to end users. MSDFS is a great management tool in that respect. All access is, of course, controlled through the MSDFS root server (the one with all the redirection points on it).
Another way one can securely collect/centralize Windows Share data is by use of a tool like rsync. Using this tool one can give users in each office read/write access to their own data, and give all other offices read-only access from a copy of that data that updates regularly using rsync. Only the changes to the data need to be transferred between the point of origin and the various destination systems. Rsync can be run over ssh for increased security.
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