*** NO! *** don't change prefixes!!!! Changing prefixes to a database involves a lot more than just changing the line in the config.php file of a moodle site.
Check the config.php files of all the instances.
Check DB name ... they all should be different database names.
It's perfectly fine for different databases to have the same prefix.
Here's site that has several Moodles - note each has a different database name:
[root@sos html]# fgrep 'dbname' ./moodle*/config.php
./moodle27/config.php:$CFG->dbname = 'moodle27';
./moodle30/config.php:$CFG->dbname = 'moodle30';
./moodle31/config.php:$CFG->dbname = 'moodle31';
./moodle32/config.php:$CFG->dbname = 'moodle32';
./moodle33/config.php:$CFG->dbname = 'moodle33';
but their prefixs are all the same:
[root@sos html]# fgrep 'prefix' ./moodle*/config.php
./moodle27/config.php:$CFG->prefix = 'mdl_';
./moodle30/config.php:$CFG->prefix = 'mdl_';
./moodle31/config.php:$CFG->prefix = 'mdl_';
./moodle32/config.php:$CFG->prefix = 'mdl_';
./moodle33/config.php:$CFG->prefix = 'mdl_';
I told you to check the databases with 'show tables' from a db client. Check the output of the following mysql command to see if there are any tables that have a different prefix:
mysql> use moodle33;
mysql> show tables;
That will scroll and finally stop to return you to the mysql prompt and above you will see something like (maybe not exactly - something like):
| mdl_workshopallocation_scheduled |
| mdl_workshopeval_best_settings |
| mdl_workshopform_accumulative |
| mdl_workshopform_comments |
| mdl_workshopform_numerrors |
| mdl_workshopform_numerrors_map |
| mdl_workshopform_rubric |
| mdl_workshopform_rubric_config |
| mdl_workshopform_rubric_levels |
381 rows in set (0.00 sec)
See the mdl_ in front of the table names .... that's the prefix.
Do that for each database for each moodle instance.
Please don't jump at what's suggested you check out. Check it out first!!!!
I hope you've started working this out by backing up databases - even if there might be something wrong in them right now. We need to attempt to resolve the reason ... rather than taking a sledge hammer approach it might require something more like a finishing hammar.
Mind you ... not that I would know exactly what to do, cause I've never heard of the situation you've desribed.
'spirit of sharing', Ken