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The Doc Filter Connector has an important limitation ! If you use it on several jobs having the same repo source connector to filter different kind of files (like one job to only include pdf files, and one job to only include office files), the filters will conflicts. The result is that only the files matching the filters configured on the last ran job will be indexed, the files matching the filters of all the other already ran jobs will be deleted from the index !

For example, if you have 2 jobs configured with the same repo source connector, one job that only includes pdf files, one job that only includes office files, if you run the pdf files job first, then the office files job next, your index will only contains office files, not the pdf ones.

To solve this issue, you need to use a different repo source connector per job ! Yes it means to have several repo source connectors that are strictly identical BUT their names. Unfortunately, there is no other solution as it is a MCF framework limitation that causes that behavior.