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There may be several approaches to your dilemma; here is my response as a Stabilitarian for an interim action, but I would also suggest that you immediately contact the manufacturer of your chamber or an organization that specializes in chamber maintenance.
The 3 out of specification readings should be documented in your quality system and be subject to immediate remediation. Some would relocate their samples to an alternate qualified chamber. Others might tag those problematic locations and not place samples there in that specific chamber.
While waiting for a plan of action from your chamber supplier/maintenance organization, you may consider lowering your 65% setpoint to 63% to see if that brings the high points into compliance (without dropping below 60% at your lower points). You may also increase air circulation to mix the air and hence the humidity, which may give you a more balanced set of readings throughout. Neither of these should be considered a long term solution, but actions taken on a temporary, quality-guided basis to preserve the integrity of your studies.
I would thoroughly document what the problem was and what steps you took to resolve it, including approvals by your quality assurance colleagues and change control staff. You may also consider creating a story board for the situation that you could use if questions were raised during a regulatory inspection.
Your second question raises a good point. The accuracy of all our measurements is based upon the cumulative margin of error of all equipment and instruments involved. That is why the plus/minus range for relative humidity in chambers is a relatively wide 5%. We take those variations into consideration when determining our setpoints, calibration targets, etc, but it would be risky to base our on the spot decisions on those margins. Regulatory inspectors would see it as a way to avoid proper corrections. The best practice would be to make sure that the data-loggers are kept within calibration parameters and then rely on their measurements, while acknowledging their margin of error.