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@Sharma, Praghya (CONTRACTOR) - Thanks for the question and using MS Q&A platform.
There is no limit on the number of columns that can be mapped using custom rules in Microsoft Purview. However, there are a few things to keep in mind that may affect the mapping of columns:
Make sure that the custom rules are defined correctly and are targeting the correct columns. If the rules are not defined correctly, then the columns may not be mapped correctly.
When running an incremental scan, only the changes since the last scan will be picked up. If the columns were not mapped in the previous scan, then they will not be picked up in the incremental scan. You may need to run a full scan to ensure that all columns are mapped.
The mapping of columns may also depend on the data type and format of the columns. If the data type or format of the column is not recognized by Purview, then it may not be mapped correctly.
In your case, since you have 900+ columns and only 400 columns were not mapped in the incremental scan, it is possible that the custom rules are not targeting the correct columns or the data type or format of the columns is not recognized by Purview. I would recommend reviewing the custom rules and the data types and formats of the columns to ensure that they are defined correctly. If necessary, you may need to run a full scan to ensure that all columns are mapped.