If you have local edits in your cctbx_project directory, you'll need to copy them over to your new folder.
More detail for those interested. The following example illustrates the problem:
[phenix-src/cctbx_project/scitbx/lstbx]$ svn update
[phenix-src/cctbx_project/scitbx/lstbx]$ svn status
According to svn, this directory is up to date
[phenix-src/cctbx_project/scitbx/lstbx]$ svn info normal_equations.h
Path: normal_equations.h
Name: normal_equations.h
Repository UUID: 3c1a6239-ac2c-0410-bc49-92500e444112
Revision: 22630
Node Kind: file
Schedule: normal
Last Changed Author: luc_j_bourhis
Last Changed Rev: 15039
Last Changed Date: 2012-03-12 10:03:05 -0700 (Mon, 12 Mar 2012)
Text Last Updated: 2015-07-27 10:24:16 -0700 (Mon, 27 Jul 2015)
Checksum: ec2e555a9ad1d2553bb37bc04f677ef5
Note the revision number is 22630, and it lists the last revision for this file as 15039. After I move my directory aside and re-check out the directory:
[phenix-src/cctbx_project/scitbx/lstbx]$ svn info normal_equations.h
Path: normal_equations.h
Name: normal_equations.h
Repository UUID: 3c1a6239-ac2c-0410-bc49-92500e444112
Revision: 22630
Node Kind: file
Schedule: normal
Last Changed Author: nksauter
Last Changed Rev: 22624
Last Changed Date: 2015-07-25 17:16:55 -0700 (Sat, 25 Jul 2015)
Text Last Updated: 2015-07-27 10:46:36 -0700 (Mon, 27 Jul 2015)
Checksum: e5e5e623ecdde362afadf321d37b2c5e
The correct revision is now retrieved.
Thanks,
-Aaron