I want to say I used to have a similar problem with...amdgpu-dkms, maybe?  
Where a reinstall or update operation wouldn't work right, seemingly because 
the cleanup for the previous version of the package would wipe out what the new 
one installed, so my procedure became to remove and install in two separate 
operations.  Whether it was the fault of DKMS itself or of amdgpu-dkms' 
packaging, I don't know, but even if it's the latter it suggests to me that 
DKMS doesn't make it easy to package robustly.
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