My Content Type instances have duplicate Document IDs (dlcdocid).

I’m not sure I fully understood your question but let me share my experience.

First, I’m not completely sure where you enabled the Document ID feature, but this part is important. If you’ve turned it on in the Content Type Hub site collection, that’s usually not recommended. My suggestion is: do not enable the Document ID feature in the Content Type Hub. Instead, enable in the Teams sites where you are actually creating and storing documents for collaboration.

I never upload the template into the Content Type Hub and keep the default template there. However, in the target site / library where I’m using that content type, I upload the template using the Add Template option at library level.

For template management, I always maintain a separate site - Templates and Forms Center, where the Document ID feature is not enabled. The reason is simple: you don’t have control over how IDs are stamped in templates, and this avoids duplication issues.

Another point: for metadata, I keep things very specific. For example, in my Templates library I don’t use a generic column like Status. Instead, I create a column called Template Status, because in my target library the meaning of Status might be different. But if there’s a property I want to be inherited into documents created from the template, I use the same column name in both locations. That way, the property flows correctly from the template into the document.

Here is the solution for your issue, please try it and let me know if it works.

• The Document ID service assigns IDs when a document is first added to a library. If your template file already has a Document ID property embedded, new documents created from it will inherit that value. Because the Document ID field is read‑only, you can’t manually clear or overwrite it once it’s stamped.

• Clear the Document ID from the Template and Upload the clean template (without Document ID) to the Hub.
  • Open the template in Word.
  • Go to File > Info > Properties > Advanced Properties > Custom tab.
  • Look for _dlc_DocId or related fields.
  • Delete those custom properties.
  • Save the template back to the Content Type gallery.
  • This ensures new documents don’t inherit a fixed ID.
• Unfortunately, you cannot directly edit the Document ID field.
• Options:
• Clear Document ID and Re‑upload the documents: 
  • Download template locally, Open the template in Word.
  • Go to File > Info > Properties > Advanced Properties > Custom tab.
  • Look for _dlc_DocId or related fields.
  • Delete those custom properties.
  • Upload the template back to the Content Type gallery.
  • This ensures new documents don’t inherit a fixed ID.
• Use PowerShell/CSOM/Graph API: Admins can script a re‑index or re‑assignment (any different value) of Document IDs by forcing the Document ID service to re‑run.

If my post solved your issue or answered your query, please mark it as a Solution and give it a Like.