Although this can not be done in bulk, there is a way to do this directly in MYSQL, which is far quicker than using JIRA.
Back-up the MySQL database
Find Table "configurationcontext"
identify the custom fields to update (e.g. customfield_13102)
enter the project id value (e.g. 10900) into the field PROJECT.
Once all custom fields are updated with the project ID's you will need to restart the JIRA instance
ARGH! NO! You're missing half the process, and this could completely wreck the Jira instance. Backups good, yes. But... NEVER NEVER NEVER write to a Jira database while it is running. You MUST shut down Jira before you take the backup If you add any contexts, you will also need to update the sequence tables. After restarting Jira, you MUST perform a full re-index as well.
Oh, and SQL is always a last resort. The general advice for using SQL on Atlassian products is "don't". Rescuing systems that have been damaged by someone running SQL, even really simple stuff, has got me several jobs in the past. It's a nightmare fixing them. Don't. Just don't.
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