I do not see any issues as such. All I recommend you is to run the upgrade compatibility check list which would provide you the feasibility study, based on which you could proceed further wihtout having any issues.
Re: upgrading ePO version 5.3.1 to 5.9.1 in production
During the upgrade, apache services are off, so systems will not be able to connect to epo for any policy changes. They will use the policies they already have on their system, so there should be no issues in that regard.
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