Update LoadedApk instead of re-creating on outdated cache

Recreating the entire object drops the mApplication inside,
so multiple Application instances are unexpectedly created.

Instead, call into updateApplicationInfo to replace
the Resources object manually.

Bug: 129890769

Test: device boots, applies overlay paths correctly; was unable
to reproduce a case where the overlays are missing from the
system itself, other Resources/caching changes may have
decreased the occurrence rate

Change-Id: Ib5e7d6ca79ac5b37d5691ce327e3b66cc4672335