mobile apps now in two locations

Before doing an "secure empty trash", I looked through the contents and found a HUGE qty of .ipa files.

Before securely emptying the trash, I did a search for all files with ".ipa" in the name.

The ones saved from the trash, now in a file on my desktop are generally NEWER than the others (in iTunes file?).

Might be that I'm temporarily using an older 3G iPhone?

WHAT SHOULD I DO with mobile apps since they're now in two locations in different versions?

MacBook Air

OS 10.9.4 (13E28)

1.7 GHz Intel Core i5