Custom Menu items are stored in the mdl_config table of the database per moodle site.
select * from `mdl_config` where `name` like "custommenuitems"
Are both sites pointed to the same database? Check the config.php file for both sites to confirm they are not.
Might also purge the cache on both sites ... not supposed to happen but ...
'spirit of sharing', Ken
It's an sql query that will show the links of custommenus.
Run it via phpmyadmin or whatever you use for the DB. Also run it against the databases for the two sites where the links appear the same.
Site A: uses moodleSiteA DB ... run query vs that database. Note the URL's in the custommenus.
Site B: uses moodleSiteB DB ... run same query vs that database.
If Site A and Site B both use the SAME database, that's why the custommenus are the same on both sites.
'spirit of sharing', Ken
Ok, we'll forget about the 'techie lingo'. Maybe a suggestion that one learns how to use PMA [assume that means phpmyadmin] to use those sql queries shared earlier).
However, concentrating on this last posting.
"it would have been through the front end (through Moodle, rather than through cpanel, PMA, or other)"
If Bluehost can't figure it out then ....
But ... will pose some simple questions:
Assuming you installed them all ... all three ... and that you did not use any app provided by Bluehost to install ... basically *each* moodle site requires a unique code directory, a unique data directory, and a unique database.
So ... three moodle sites - A, B, C
Siite A
domain is moodlesiteA.somenet.net
code directory is in /customer/webrootsiteA/
data directory is in /customer/siteAmoodledata
Site B
domain is moodlesiteB.somenet.net
code directory is in /customer/webrootsiteB/
data directory is in /customer/siteBmoodledata
Site C
domain is moodlesiteC.somenet.net
code directory is in /customer/webrootsiteC/
data directory is in /customer/siteCmoodledata
or something like that.
Compare the config.php file of each site ... siteA, siteB, and siteC ... have a feeling you'll see more than one is pointed to same data, same database at least.
What does 'your space' on Bluehost look like?
Ken
Before anyone could begin to suggest how to fix what appears to be 3 instances of Moodle on a single Bluehost domain that are mis-configured, more specific information about how those instances were installed .... ie, into what directories, etc.. and investigation of *each* config.php file for *each* instance to see where those are pointed to ... wwwroot, data directory, AND the DB to be used for *each* site.
The following is a representation ... it is probably NOT the same as what is in your space on Bluehost - but this should give you something to work from:
wtunersites - your home folder/directory
Listing below:
Directory permissions/ownership
Size
Owner
Group
name of folder
drwxr-xr-x 4 wturner wturner moodle - url for this is http://yourdomain/
drwxr-xr-x 4 wturner wturner moodle2 - url for this is http://yourdomain/moodle2
drwxr-xr-x 2 wturner wturner moodle2data
drwxr-xr-x 4 wturner wturner moodle3 - url for this is http://yourdomain/moodle3
drwxr-xr-x 2 wturner wturner moodle3data
drwxr-xr-x 2 wturner wturner moodledata
wtunersites/moodle:
total 0
-rw-r--r-- 1 wturner wturner config.php
-rw-r--r-- 1 wturner wturner moodlecodeformoodleinhere
wtunersites/moodle2:
total 0
-rw-r--r-- 1 wturner wturner config.php
-rw-r--r-- 1 wturner wturner moodlecodeformoodle2inhere
wtunersites/moodle2data:
wtunersites/moodle3:
total 0
-rw-r--r-- 1 wturner wturner config.php
-rw-r--r-- 1 wturner wturner moodlecodeformoodle3inhere
wtunersites/moodle3data:
wtunersites/moodledata:
Looks like attachment? (or sort of).

Is this (sort of) what you did? (attachment)
If so, am surprised that two of them are working at all!!!
The fix is 'technical' and am not sure the 'fix' will actually 'fix' depending upon what one finds when inspecting the config.php files for all sites and the directory/folder structure. Could involve making a copy of a data directory for one instance and creating a new instance of that data directory by another name. Same for a db ... depending upon info in config.php file comparison.
The site at domainroot is probably your original in production Moodle site. That site needs to remain. The other instances of Moodle are in folders of their own *inside* the domainroot.
Please use whatever control panel/tool you have to take a screen shot of your 'space'.
And provide clips - copy and pasted text - with labels (moodle, moodle1, moodle2) of the config.php files lines that follow giving:
$CFG->wwwroot = 'http://example.com/moodle';
$CFG->dataroot = '/home/example/moodledata';
$CFG->dbhost = 'localhost'; // eg 'localhost' or 'db.isp.com' or IP
$CFG->dbname = 'moodle';
Above are examples from config-dist.php file.
If two instances are 'tinker' sites and not intended for production, you *might* be better off removing them. But be careful IF one of the tinker sites is pointed to the SAME DB and/or data directory for the production instance ... the one you want to keep.
'spirit of sharing', Ken
