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It would be great help if you can suggest us any tool available to migrate the historical data from AX 2012 R2\R3 to D365FO.
Can we just upgrade historical data only, not code from AX 2012 to D365FO?
All data or some selected data? For all data you can do data upgrade for the database. More info in the general upgrade article: https://docs.microsoft.com/en-us/dynamics365/fin-ops-core/dev-itpro/migration-upgrade/upgrade-overview-2012
Of course it can only work for the standard tables and fields if you don't do code upgrade that would bring your custom tables and fields to D365FO.
For partial data migration you can use data entities.
Because I already replied to the same question in another thread, let me simply copy the reply here too:
You can see the data upgrade overview at the documentation page Upgrade from AX 2012 to Finance and Operations, with details at subsequent pages (such as Upgrade from AX 2012 - Data upgrade in development environments).
Yes, it's possible to do data upgrade without code upgrade, if you're willing to lose all customizations (including data in custom tables and fields, unless you can somehow put them to standard tables and fields in D365FO).
Duplication leads either to extra maintenance cost or to inconsistent data.
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