Unless I am misunderstanding you, you shouldn't need to do that?

The 'normal' way of doing things is:

--- file \this\path\gui\skills_gui.pm --
package skills_gui;
...
----------------------------------------
--- file \this\path\db\skills_db.pm --
package skills_db;
...
---------------------------------------=

--- file \that\path\gui\skills_gui.pm --
package skills_gui;
...
----------------------------------------
--- file \that\path\db\skills_db.pm --
package skills_db;
...
---------------------------------------=
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And in the calling script have

---- File: \some\other\path\yourscript.pl ---
use lib $ENV{LIB_PATH};
use gui::skills_gui;
use db::skills_db;

....
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For one run of the script set LIB_PATH=\this\path\ and it will use \this\path\gui\skills_gui.pm and \this\path\db\skills_db.pm
and for another run you'd set LIB_PATH=\that\path\ and it will use \that\path\gui\skills_gui.pm and \that\path\db\skills_db.pm.

So the one script unchanged will use either set of modules depending upon the setting of the environment variable.