A Marketo user has the ability to merge a Marketo record together with a SFDC Lead or Contact record if the Marketo user has the “Merge Leads” permission. Merging can only be done manually since the Marketo user will need to address any field value conflicts that may arise. There is no flow step to merge records in Marketo in bulk.
When you merge records in Marketo, in the case of conflicts you can choose which value to keep. If you don't want either value, you can check Custom and enter a value of your choice. Thus, you get to choose which scoring values you want or you can enter a new value.
After the Merge
The default Lead Score field and all other custom score fields are not added up since you chose the score to keep during the merge. The complete activity logs will be merged in Marketo including membership in all programs. Last Interesting Moments will be merged in Sales Insight.
Here is a detailed article by Grant Booth on understanding merges in Marketo.
When to Use Marketo to Merge Records
I recommend only using Marketo to merge records if one of the records is in Marketo only. If two or more records are in SFDC, you should use SFDC to merge the records since all the SFDC fields might not be synced to Marketo and you won't be able to address those field conflicts.
If you have a lot duplicates to manually merge, contact your CSM and ask about the Marketo AutoMerge service.
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