I don't think the game cares when you register or change cvars or execute config files. I guess I'll test it.
EDIT:
Tested, works. If I change the cvar in the file and change the map, I retrieve the new value.
PHP Code:
#include <amxmodx>
#include <amxmisc>
#pragma semicolon true
public plugin_init()
{
register_plugin("Cvars Test", "1.0.0", "KliPPy");
}
public plugin_precache()
{
new const testCvar = register_cvar("my_test_cvar", "1337");
new configFilePath[256];
get_configsdir(configFilePath, charsmax(configFilePath));
add(configFilePath, charsmax(configFilePath), "/cvartest.cfg");
server_cmd("exec %s", configFilePath);
server_exec();
log_amx("my_test_cvar = %i", get_pcvar_num(testCvar));
}