Slic3r uses ADMesh internally to validate and fix mesh. You could try to use ADMesh directly to see a limited information about what was changed. Note that Slic3r bundles it's own copy of ADMesh and depending on your Slic3r version and edition, the behavior of it's ADMesh might slightly differ from the standalone one. (For example Slic3r Prusa Editon patches it's own ADMesh very heavily.)
Using ADMesh CLI:
$ admesh cube_bad.stl
ADMesh version 0.98.2, Copyright (C) 1995, 1996 Anthony D. Martin
ADMesh comes with NO WARRANTY. This is free software, and you are welcome to
redistribute it under certain conditions. See the file COPYING for details.
Checking nearby. Tolerance= 1.000000 Iteration=1 of 2... Fixed 0 edges.
Checking nearby. Tolerance= 1.000173 Iteration=2 of 2... Fixed 0 edges.
Removing unconnected facets...
Checking normal directions...
Checking normal values...
================= Results produced by ADMesh version 0.98.2 ================
Input file : cube_bad.stl
File type : ASCII STL file
Header : solid cube (repaired)
============== Size ==============
Min X = 0.000000, Max X = 1.000000
Min Y = 0.000000, Max Y = 1.000000
Min Z = 0.000000, Max Z = 1.000000
========= Facet Status ========== Original ============ Final ====
Number of facets : 12 12
Facets with 1 disconnected edge : 3 0
Facets with 2 disconnected edges : 0 0
Facets with 3 disconnected edges : 1 0
Total disconnected facets : 4 0
=== Processing Statistics === ===== Other Statistics =====
Number of parts : 1 Volume : 1.000000
Degenerate facets : 0
Edges fixed : 0
Facets removed : 1
Facets added : 1
Facets reversed : 2
Backwards edges : 0
Normals fixed : 2
The statistics should give you some idea about what happened.
Find ADMeshGUI at github.com/admesh/ADMeshGUI.
Open the file and click the REPAIR button in bottom right. See the changes.