It didn't work because there are hard coded references to the bakery folder in the source code and possibly in the database too. Once the module is installed, it gets really complicated to find all of the right spots. That's why it's better to make the changes before you install it.
Doing a search and replace for the uppercase of "BAKERY" is probably not necessary. Based on my quick scan, it seems to only be used for $MOD_BAKERY variables but I could be wrong.
The mixed case "Bakery" is typically only used to refer to the name of the Bakery module itself. Again, you can probably get away with not changing this except in the "info.php" file where you must if you want to specify a separate installation of Bakery if you are going to change the database prefix and run multiple copies of Bakery. This affects the name of the page type when you are creating a new page.
Where it gets more complicated is when it comes to the lowercase "bakery". Unfortunately this string is used in many situations including but not necessarily limited to the folder name and the database table prefixes.
For example, I just did a search for "modules/bakery" throughout all of the files and found that 63 of the bakery module files included that specific string alone. The folder name also appears in "info.php". If I search for just lowercase "bakery", it shows up in 135 files which obviously includes those found in the modules/bakery search above.
It would be nice to replace all this with one variable in the info.php file and be able to easily modify it in just one place. This would make it easier to change the folder name.
While we are at it, it would also be nice to have a variable for the database table prefix. This would allow us to have more than one instances of the bakery module installed at a time.
Keep in mind that I spent a total of about 5 minutes doing this research so I may have missed a few things along the way. If you use this information, your mileage may vary. If you do try your hand at it, let us know what worked, what didn't for you.
As usual, take what makes sense to you and forget the rest.
With best regards,