It’s best to transplant or re-pot a peace lily right at the start of the growing season, in the early spring. While it’s safe for the peace lily you may lose any blooms, as this coincides with the start of the flowering season. Blooming is hard work for a plant. It requires a stable environment, especially at the roots. Unpotting your peace lily is deeply stressful, and it’s likely the plant will respond to the stress by sacrificing its flowers.