I am still working in the last agency created through reorganization (DHS). Morale has never recovered, but I can tell you that employees in organizations with a strong culture and important missions (e.g. USCG, USSS, CBP, and FEMA) were able to succeed despite the reorganization. The projected savings in overhead (HR, IT, etc.) was never realized because each component kept these functions.
I would recommend that leadership be constantly present and keep communications open with employees during the process. The new mission should provide a compelling purpose (e.g. protecting the homeland) and employees who are performing mission-critical work need to be appreciated. Cultures need to be honored and the rationale behind decisions must be explained to employees impacted. Also, please don’t make decisions for “political” reasons, but for the good of the service.