Yes, that can be frustrating. Just as in Eclipse, the installation stops or crashes because it is unable to find one file.
There is a way around this. Instead of selecting to 'Help => Check for Updates', select 'Help => Install New Software'. Then follow these steps:
1) Click on Add. Then add the following respective values for name and location:
That is the current URL of the update site.
2) Click on the link Available Software Sites. You will get a user interface showing the list of available update sites. The list includes the site you have just added, CFBuilderUpdate20170207.
3) Uncheck all checkboxes, except the checkbox for CFBuilderUpdate20170207.
4) Click on File menu, and select Restart.
5) Select Help => Check for Updates