It should be possible in the clock section of the DWR to set the actual WCO frequency. If not, you might raise a support case with Cypress (top right corner, 'MyCases')
Well, I can't modify it by clicking/right-clicking on it. If I double-click, it opens the "Configure System Clocks" on the "Low Frequency Clocks" tab, but I can't modify the value of the WCO frequency.
What's the normal method to change it?
Oh, I forgot that on the BLE the WCO is internal to the chip (on the PSoC5 its an external crystal so you can actually set the frequency). I think your method will work, but to be sure you need to ask Cypress.
You might try to change the selected device (e.g. to a 4200L device or so) and see whether this will overwrite the setting. If not, you can always recreate the project from scratch and copy over the schematic and the code.
Even though the table in the Design Wide Resources file says that the WCO frequency is "32kHz", it is actually "32.768kHz". So, you don't have to modify anything unless you want the table to read 32.768. You don't have to modify anything, PSoC knows that the WCO frequency is 32.768kHz and it is expecting the same.