We have project sites automatically provisioned in our SharePoint based on a user action and as part of the site we enable the document id feature and use a custom prefix. Now I know the document id feature relies on 2 timer jobs and it seems on our environment they are set to run once a day. The problem with this is if users upload documents and don't check them in then when the job runs the document id's are not updated with the prefix. Is it a bad idea to set these jobs to run more frequently? Has anyone done this and if so did they encounter any problems and how often did you set them to run?
Document ID enable/disable job
This will process all work items on all site collections in a web application, and make sure that Document ID prefix is pushed to all subsites. Document ID field will be added to all content types which inherit from Document and Document Set. More precisely, three fields will be added: Document ID, Document ID Value and Persist ID. In addition to adding these columns, SharePoint adds an event receiver to each of the content types so that they run every time a document or document set is uploaded to SharePoint. The server uses ItemAdded event to ensure that document ID providers can use item metadata when assigning document IDs.
The default schedule: Every day 21:30-21:45
Document ID assignment
This will push the settings to all lists and assign Document IDs to the documents.
The default schedule: Every day 22:00-22:30
I believe you don't need Document ID enable/disable job to be run more frequently, while running Document ID assignment more often might help. I've done this before (set it to run 4 times a day) and haven't noticed any problems.