One shouldn't 'over write' anything in moodle code ... core or plugin. Like core code when one updates, current code should be archived, and a fresh code directory for plugin used.
Plugins should store their settings in the DB ... mdl_config_plugins.
Now you've said you collected all the updates to plugins?
Share with you what I do prior to upgrading core code.
1. install moosh
https://moodle.org/plugins/view.php?id=522
2. in code directory (since I use git to maintain and update code my code directory doesn't move), create a text file that list the short names of the plugins called 'addons.txt'.
Looks like:
mod_game
mod_hotpot
mod_mootyper
mod_taskchain
filter_poodll
qtype_poodllrecording
atto_poodll
atto_subtitle
3. create a bash shell script called 'checkaddons' that contains:
#!/bin/bash
#
echo 'Add-on listing: ';
cat ./addons.txt;
echo '---------------------';
for i in `cat ./addons.txt`
do
echo "Addon in que: $i";
moosh -n plugin-list |grep $i
done
When run like ./checkaddons displays
Add-on listing:
mod_game
mod_hotpot
mod_mootyper
mod_taskchain
filter_poodll
qtype_poodllrecording
atto_poodll
atto_subtitle
---------------------
Addon in que: mod_game
mod_game,2.0,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/22090/mod_game_moodle39_2020072501.zip
Addon in que: mod_hotpot
mod_hotpot,2.0,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,https://moodle.org/plugins/download.php/21609/mod_hotpot_moodle38_2020060544.zip
Addon in que: mod_mootyper
mod_mootyper,2.2,2.3,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/21941/mod_mootyper_moodle39_2020070800.zip
Addon in que: mod_taskchain
mod_taskchain,2.0,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,https://moodle.org/plugins/download.php/21610/mod_taskchain_moodle38_2020060589.zip
Addon in que: filter_poodll
filter_poodll,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/21827/filter_poodll_moodle39_2020062400.zip
Addon in que: qtype_poodllrecording
qtype_poodllrecording,2.1,2.2,2.3,2.4,2.5,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/21745/qtype_poodllrecording_moodle39_2020061600.zip
Addon in que: atto_poodll
atto_poodll,2.6,2.7,2.8,2.9,3.0,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/19977/atto_poodll_moodle39_2019071300.zip
Addon in que: atto_subtitle
atto_subtitle,3.1,3.2,3.3,3.4,3.5,3.6,3.7,3.8,3.9,https://moodle.org/plugins/download.php/20669/atto_subtitle_moodle39_2019112101.zip
from that redirected to a 'getlist' file
./checkaddons > getlist
which would need to be edited to contain just the url to the plugins:
'getlist' looks like:
https://moodle.org/plugins/download.php/22090/mod_game_moodle39_2020072501.zip
https://moodle.org/plugins/download.php/21609/mod_hotpot_moodle38_2020060544.zip
https://moodle.org/plugins/download.php/21941/mod_mootyper_moodle39_2020070800.zip
https://moodle.org/plugins/download.php/21610/mod_taskchain_moodle38_2020060589.zip
https://moodle.org/plugins/download.php/21827/filter_poodll_moodle39_2020062400.zip
https://moodle.org/plugins/download.php/21745/qtype_poodllrecording_moodle39_2020061600.zip
https://moodle.org/plugins/download.php/19977/atto_poodll_moodle39_2019071300.zip
https://moodle.org/plugins/download.php/20669/atto_subtitle_moodle39_2019112101.zip
You might note that depending upon when one does checks on plugins, the plugin files (zips) might actually show a filename of version higher that what you are running for code. As long as it's listed as being compatible.
4. use wget to acquire all the zips
Now you have the zips to use when upgrading those plugins ... if doing so manually.
You could let moodle get the updates to all your pluings if not doing manually.
After upgrading, go to Notifications and check for updates.
It should see plugins that need updating ... follow that link and update the plugins that way.
'SoS', Ken