The issue if I understand it is that Excel is not listed as a Supported Format Type in Acrobat Pro. When you are combining files, you should be able to combine any of the Supported File Types, such as PDF, Word, Excel, PowerPoint, etc.
This is what it should look like when you go to Tools > Combine Files > Add Files

But in a recent update to either Acrobat DC Pro or Office 2016, Excel is no longer listed as a Supported File Type and attempting to combine them will result in an error.
I was running into the same exact issue. Microsoft says it's an Adobe issue. Adobe says it's a Microsoft issue. Neither were of any help. I have tried to un-install and re-install both, and for some machines, rolling back to an earlier version of Office worked. But not in all instances. How I fixed it was copying the registry key from a machine that worked to a non-working machine.
To have .xls files show as a Supported File Type in Acrobat DC this is the registry key that I copied and replaced:
Windows Registry Editor Version 5.00
[HKEY_CLASSES_ROOT\.xls]
@="Excel.Sheet.8"
"Content Type"="application/vnd.ms-excel"
[HKEY_CLASSES_ROOT\.xls\PersistentHandler]
@="{98DE59A0-D175-11CD-A7BD-00006B827D94}"
[HKEY_CLASSES_ROOT\.xls\ShellEx]
[HKEY_CLASSES_ROOT\.xls\ShellEx\{8895b1c6-b41f-4c1c-a562-0d564250836f}]
@="{00020827-0000-0000-C000-000000000046}"
For .xlsx files:
Windows Registry Editor Version 5.00
[HKEY_CLASSES_ROOT\.xlsx]
"PerceivedType"="document"
@="Excel.Sheet.12"
"Content Type"="application/vnd.openxmlformats-officedocument.spreadsheetml.sheet"
[HKEY_CLASSES_ROOT\.xlsx\Excel.Sheet.12]
[HKEY_CLASSES_ROOT\.xlsx\Excel.Sheet.12\ShellNew]
"FileName"="C:\\Program Files (x86)\\Microsoft Office\\Root\\VFS\\Windows\\ShellNew\\excel12.xlsx"
[HKEY_CLASSES_ROOT\.xlsx\PersistentHandler]
@="{4887767F-7ADC-4983-B576-88FB643D6F79}"
[HKEY_CLASSES_ROOT\.xlsx\ShellEx]
[HKEY_CLASSES_ROOT\.xlsx\ShellEx\PropertyHandler]
@="{33154C99-BF49-443D-A73C-303A23ABBE97}"
[HKEY_CLASSES_ROOT\.xlsx\ShellEx\{8895b1c6-b41f-4c1c-a562-0d564250836f}]
@="{00020827-0000-0000-C000-000000000046}"
[HKEY_CLASSES_ROOT\.xlsx\ShellEx\{BB2E617C-0920-11d1-9A0B-00C04FC2D6C1}]
@="{72B66649-3DBF-429F-BD6F-7774A9784B78}"