Microsoft Dynamics GP >> Utilities >> Inventory >> Remove Transaction History
All it does is remove the transaction from Inventory History Tables. If you are going to use Site Combiner loosing this History is a moot point. It has no effect on GL, Inventory balances, etc. - unless you don't follow through with the Site Combining. Then you may (or may not) have a problem. Removing the History, removes the warning which then allows you to proceed with Site Combining.
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Tim