Ideally, a protocol/proposal should be published before data collection starts, however, there is no policy against publishing protocols/proposals when data collection is already underway or completed, or even after the primary paper has already been published, as long as this is made explicit in the manuscript. Inversely, there is no policy against publishing protocols of research that is not funded yet (although in this case, the 50% discount does not apply), or when there is no ethics approval in place yet. The key is transparency in reporting in regards to the status of the research at submission.
In the "Results" section of your protocol (both abstract and the main manuscript body), please explicitly state the current status of the project (e.g. "Funded in X, data collection started in Y and is expected to complete in Z | data collection has been completed in Z)").
Since 2018 we have incorporated IRRIDs (What is a International Registered Report Identifier (IRRID)?) into our Research Protocols, so at the time of submission you will have to declare the stage at which the study is in terms of data collection and analysis (DE=Data existing, if you already started enrolment of participants or collected data, PRE=submitted before data collection).
Related:
- Where should I publish what, and what should be my research and publication strategy to maximize impact and dissemination of my ehealth/mhealth/digital medicine research?
- Why should I publish my protocol or grant proposal?
- Which of your journals publishes protocols?
- When is a grant proposal or protocol eligible for the 50% discount on the APF?
- What is the impact factor of JMIR Research Protocols?