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Best to ask Support so you can get more details about the error, but yes, it could be too much data load at one time that caused the error.
If you remove a field from the Marketo sync user that already has values for leads in Marketo, they will remain with those values but they will never have them updated from SFDC. So it is best to hide those fields if you don't intend to use them again. Note that you need to remove all references to that field in forms, smart lists, and smart campaigns before you can hide a field.