I assume your script is opening the modules, so all you need to do is check if it is already open first.
string sModuleFullName = "/Some/Module/Path"
Module oModule = module(sModuleFullName)
bool bClose = null(oModule)
if(null(oModule)) {
oModule = read(sModuleFullName, true,true)
}
// do stuff
if(bClose) {
close(oModule)
}
Edit: Alternative method for closing modules opened by triggers, attribute or layout dxl
// Save currently open Modules to a Skip
Skip oOpenModulesSkip = createString()
Module oModule
for oModule in database do {
put(oOpenModulesSkip, fullName(oModule), fullName(oModule))
}
// do stuff
// Close Modules not in the Skip
for oModule in database do {
if(!find(oOpenModulesSkip, fullName(oModule))) {
close(oModule, false)
}
}
delete(oOpenModulesSkip)