it depends on how the change has been done. As far as I understand, you have added a naming series to the item DocType. For this, you have probably switched to develop_mode and used Edit Doctype. Edit DocType will alter the definition file, which will break bench update. For this, you will have to fork ERPNext and use your sources. And if you have changes valueable for others, feel free to share them.
Without edit doctype, AFAIK, there is no option to introduce a naming series to the item doctype. You could use a custom script and set the item_code based on a what items are in the system, reflecting the function of a naming series.
In short
when you use “edit doctype” the json is updated (file system) and bench update does not work
Editing the doctype in developmer mode will create file changes, so yes - no.
You can fork ERPNext in github: go to GitHub - frappe/erpnext: Free and Open Source Enterprise Resource Planning (ERP) and as soon as you are logged in, you have the option to fork it. Then, you will need to add your fork as an additional remote to your server and switch to your repo. Note that you will have to update from the main repo yourself once you do this (bench update will only pull the most recent version from your repo)… Sharing changes after that is easy using pull requests. But if you do not feel familiar with github, maybe rather go with the customisation functions for now