Adjust file reference type in 'aapt2 convert'

When converting between binary and proto APKs in either direction, the
'aapt2 convert' command did not adjust FileReference type for entries
inside the resource table. This fix makes in-place changes of the resource
table passed to ConvertApk, which is safe since the resource table is
thrown away after the conversion.

Bug: 71854843
Test: Manual
Change-Id: Ide6e141269392db15b399db3566f18175f5133d5