Ann-Marie,
early on in my Callcentre career, we migrated from a Green Screen gui to a windows based system.
generally the biggest concern is that once you move away, what functionality is gained/lost and how well it is explained to the Agents. Where I worked it started with each area of the business fully documenting everything that was completed on the system and then cross checking to ensure the new system still maintained that ability.
I think the key would be UAT and systems testing first. If you can provide some more specific details I can try to tailor accordingly.
Scott
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