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Data Upgrade from AX2009 will have 2 major stages,
one is data pre-processing which happens in the source system. Here the data is converted to shadow tables which has same schema as the target tables. Downtime is required only for a short period here while the data is copied to the shadow tables.
second is Data upgrade in the target system, where the data is copied from Source to target. You need to have downtime during this stage
You can plan for 2 days of downtime for completing a data upgrade from AX2009 to AX2012 R2 or R3