Christian Phillips, chief security officer at payment processing company Regulus and an old hand at running corporate IT departments, knows all too well the challenges of blending IT departments after a merger.

In fact, he’s doing it right now.

Regulus was acquired in April by publicly traded 3i Infotech for $100 million. Phillips now must combine two separate IT operations, complete with compliance obligations, audit continuity, security programs, and more. He likens the technical challenges of mergers to the Hippocratic oath of medical doctors: Do no harm.

“To be sure, there’s no universal checklist in these situations but security and IT ...