MacBook Pro takes an hour to start up after battery has gone flat

1. Update the software on your Mac,

    Update may come with bug fixes.

    https://support.apple.com/en-us/HT201541

2. Startup in Safe Mode. https://support.apple.com/guide/mac-help/start-up-your-mac-in-safe-mode-mh21245/mac.  

    Quote:

    It also does a basic check of your startup disk, similar to using First Aid in Disk Utility. 

    And it deletes some system caches, including font caches and 

    the kernel cache, which are automatically created again as needed.

3. Reset  SMC:   How to reset the SMC of your Mac - Apple Support   Choose the appropriate method.

    Quote:

    Resetting the system management controller (SMC) can resolve certain issues related to power, battery, fans,

    and other features.

4. Battery Management.

   How battery health management helps

   The battery health management feature in macOS 10.15.5 is designed to improve your battery's lifespan

   by reducing the rate at which it chemically ages. 

   The feature does this by monitoring your battery's temperature history and its charging patterns.

   Based on the measurements that it collects, battery health management 

   may reduce your battery's maximum charge when in this mode.

   This happens as needed to ensure that your battery charges to a level that's optimized for your usage

   —reducing wear on the battery, and slowing its chemical aging.

   Battery health management also uses the measurements to calculate when your battery needs service.

   https://support.apple.com/en-us/HT211094?cid=mc-ols-energy_saver-article_ht211094-macos_ui-04022020