I realize your post is from 2014, but wanted to provide an update for later reference. Marketo has developed a 'remove crm sync' tool, which is currently still experimental. It removes the SFDC or MS CRM sync from Marketo, including all Opportunities, Company records, Sales People, SFDC Campaigns and SFDC Activities. It can then be reconnected to another CRM. It also opens up the Company, Opportunity and Sales Person APIs if you need to do a custom sync (for example for NetSuite). The 'remove crm sync' tool is currently still 'experimental', meaning that it is not officially supported. So far we have seen good results: it can be used to remove a native sync, then create a custom sync via the REST API. It also can be used for changing from one SFDC instance to another (or Microsoft CRM), going from SFDC to MS CRM and vice versa. Switching between natively-synced CRM instances is more work than removing an old native CRM sync, because the switch also requires extensive field mapping and deduplication of new records. There is still a fair bit of work involved, but it's a lot easier than moving to a new instance, and most importantly it retains all activity data. If - for whatever reason - the tool doesn't work for your particular Marketo instance, it may still be necessary to migrate to a new instance. However, so far that hasn't been necessary.
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