This behavior is by design.
When checking the PN.ini file on a fresh install of a workstation or placing a custom PN.ini file in the ICA Client directory, the client may delete some of the original entries from the file.
The Windows operating system limits the allowable size for .ini files to 64KB. Approximately 90 application sets could be stored in a PN.ini file. Starting with Citrix ICA Client Version 985, only non-default values are stored for many of the settings. In other words, if certain values are not changed during the initial configuration, they are deleted from the PN.ini file. If the value for an entry is modified to something other than the default, the entry remains or is re-added to the PN.ini file.
For example: If the HRES/VRES values are changed with the custom PN.ini, when the values are read back in, the defaults are assumed for entries that are not present. This results in the same settings as before this change was attempted. Change the HRES/VRES from the client GUI to achieve the desired results.