Thank you for details.
If we understand you correctly, you need to set up a boolean flag for successfully processed records after a package run. We can offer you the following solution.
You need to set up two import packages: one from Salesforce to MySQL with INSERT operation and another one from MySQL to Salesforce with UPDATE operation.
In MySQL table you need to create an additional ID column that will store Salesforce IDs, for example, SF_ID, and a column that stores the date of record creation, for example, createdDate.
In the first package, createdDate column should be mapped with this expression: GETUTCDATE()
This will insert actual date of record creation each time a package runs. An expression mapping can be use for that.
More details about it here.
SF_ID should be mapped to standard Salesforce ID column.
Second package from MySQL to Salesforce should have a filter createdDate >= LAST_RUN.
More details about filters you can find at this link.
SF_ID should be mapped to the same Salesforce ID column.
A column that stores flags should be mapped with a constant "true".
More details about constant mapping here.
Please note that the second package will be used for updating flags only. No other fields should be mapped there.
The time difference in schedule for packages should be around 20 minutes. Suppose the first package runs at 12:00 once an hour, then the second package should be set to run at 12:20 once an hour.
For set up such schedule, you need first click "Set time restrictions"
And then set these options.
This way all records that are moved to MySQL in the first package, will be flagged as true by second package.
Should you have any questions, do not hesitate to contact us back.