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This pipeline is supposed to be carrying Lubricant. After cutting off the supply for remodelling, all the lubricant was drained from the pipeline. Due to some engineering incompetence (oops), the pipeline was instead filled with Light Oil instead. No matter: I can find fix this and then click the Flush Pipeline button on the nearest pipe to remove all the Light Oil from the system.

That removes it from the pipes, but the internal buffer inside the pumps is not flushed. And since the pipes are carrying lubricant, the pumps can't spit their light oil out anywhere. Since they can't spit it out, they can't accept new lubricant, and thus can't do their job as pumps: they are completely stuck.

Fortunately, this can be fixed in-game: either by deleting and reconstruct the pumps, or setting the filter of the pumps, but neither of these should be needed.

What I would expect to happen: Flushing a pipeline will also delete the buffer of any pumps that have their inlet (not outlet) connected to this pipeline, or alternatively there is a Flush button on pumps.

Unfortunately I did this fix before thinking to save and post a bug report, so I reconstructed it in the sandbox:
and log file for this The pump is obviously supposed to be supplying water to the water pipeline for the boiler line, but the pipeline has been partially filled with steam (controllable with the pump up the top). Selecting the pipe and flushing it will remove the steam from the pipe, allowing the water to be connected again, but the pump's internal buffer is stuck with steam: and it requires the above tricks to be fixed and start pumping water into the boiler line.

This is working as intended - the flush pipeline button only flushes the pipeline, which is the set of connected pipes. The pumps are not members of the pipeline.

Moving to feature requests.

For what it's worth, I tentatively plan to add fluid contents and a flush button to the pump GUI, since I have run into this same situation before and was annoyed that I had to remove and replace the pump to clear it.

I think that's a workaround for the problem, not a convenient solution. It means that after a flush, all connected pumps need to be manually checked and flushed as well — and as shown in the picture, there can be many of them and/or spread out across a base.

A more convenient solution would be for all outgoing pumps (carrying the same content) to be flushed automatically as well.