The myth about battery calibration -
Your phone does not trickle charge.
It runs off of the battery at all times.
Even while on the charger.
When the battery hits full charge, it shows 99 to 100%, stops charging, and runs until it hits the set point established by HTC - these days, typically about 96%.
Then charging kicks back on and the cycle repeats itself. Over and over until you take it off of the charger.
And it shows 99 to 100% the whole time.
After you take it off of the charger, over the course of several minutes, it adjusts the user display until a more accurate reading is available.
Your phone doesn't lose 5% in minutes - it didn't have it when you took it off of the charger.
People used to post videos of a current meter showing the cycle with the screen display being constant. I haven't seen one lately, but that's the way it works.
It's due to the nature of the safety circuit involved in charging.
Do not run your phone dry unless you need to as a normal matter of use - it degrades the battery.
And to help you, your HTC will shut down before you truly hit 0% anyway.
If power consumption is different after an update, then it's likely services have changed or an app is less than optimal with the new version.
To find out, I recommend GSam Battery Monitor.
Getting a clean slate after an update is always the right idea.
It's easy if you're rooted - wipe cache and Dalvik.
If not rooted, I suggest Helium Backup, then a factory data reset (do not erase your internal storage, just reset) and then restore from the backup.
Hope this helps.