WSUS replica server fails to sync with upstream server

Initially our wsus servers version 3.2.7600.226 (2) are synchronizing properly with upstream (3.2.7600.226 also ) that run for a few years, then database size started to grow about 97 GB. Now  2 replica server  (windows 2003 standard) failing to synchronize with the upstream server (windows 2008 standard) it says connection error, an error trying to connect the wsus server. When I perform server cleanup, database error, an error occured trying to perform a database operation. However if you untick this is a replica of the upstream server, it quickly sync and succeeds. I have tried WSUS_Cleanup_CL.exe, WSUS_Driver_Decline.exe and WSUSUTIL nothings helps. Should I  better leave this is a relica of the upstream server untick it syncs and succeeds, what will be the impact, difference if this is untick?
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Bruno PACIConnect With a Mentor IT ConsultantCommented:

The difference is that computer inventory database will not be pushed up to the main stream server.

It will be like you have 2 different sites, each onu with its own database of computers and not database consolidation between them.

When you say the database is 97GB are you talking about the computers database that stores the computers inventory or are you talking about the patches datastore that contains downloaded patches ??

If the problem comes from the patches synchronization only then your can change your configuration so that only computers inventory database is synchronized, but patches are download directly from MS WindowsUpdate by both servers.
Of course this will require twice downloads from Internet (one for the upstream server, one for the child server) but until you find a better solution or find a way to clean you patch datastore it may help.

By the way, emptying the computers inventory database completly is not a big loss because computers will resubscribe to their WSUS server and upload their inventory information. So in case of a total loss, the inventory database will be recreated automatically in a few hours or a few days.

So if your inventory database is so huge because it contains a lot of obsolete computers (I can't believe it's the computer inventory that is so huge... I'm pretty sure you're talking about the patch datastore) your may find a way to restart from a blank inventory.

If you want my personal opinion, uninstalling the WSUS server, removing all the files (database and patches) and reinstalling WSUS is a few hours affair (less than a day). I wouldn't spend too much time on diagnose and probably I would decide to reinstall from scratch. It's my opinion because I know WSUS just enough to know that inventory will be recreated easily after one or 2 days. But you problem is that probably the trouble comes from the content of the upstream server. Can you manage this one ?
vanderfieldAuthor Commented:

97 GB represent downloaded patches, our branches (replicas servers) cannot redownload because of bandwidth issues, tried the export and import but unsuccesfull, any other advice?
vanderfieldAuthor Commented:
I have uninstalled and reinstalled WSUS then scheduled the downloads after hours
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