From my experience with saving groups with apps that support tabs natively, such as PDF-XChange and Foxit PDF Editor, it doesn't save said apps' tabs correctly, and only grabs the first instance. This is when using the "saved group" command from the top-bar menu.

However, I have been able to edit the .groupy file manually and add the files back in to make it work, it's rather irksome that I have to do this every time, however, since the normal way is broken.

Here's what my file looks like after it's been edited by me manually (functional):

[Group]
GroupCount=7
GroupLeft=1902
GroupTop=22
GroupRight=3802
GroupBottom=1029
GroupMax=1
Locked=0

[GroupyEntry1]
OwnerProcess=C:\Program Files\Microsoft Office\root\Office16\WINWORD.EXE
APPID=Microsoft.Office.WINWORD.EXE.15
NewTabName=
RunElevated=0
Target="D:\$\Documentation\Books\@Study Notes\Biblical\The Holy Bible - Notes.docx"
NoPatternMatching=1
MatchingClass=OpusApp

[GroupyEntry2]
OwnerProcess=C:\Program Files\Microsoft Office\root\Office16\WINWORD.EXE
APPID=Microsoft.Office.WINWORD.EXE.15
NewTabName=
RunElevated=0
SavedColour=33023
Target="D:\$\Documentation\Books\The Book of Exodus (1974) - Brevard S. Childs\The Book of Exodus (1974) - Brevard S. Childs (Converted).docx"
NoPatternMatching=1
MatchingClass=OpusApp

[GroupyEntry3]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Religion\Biblical Names Pronunciations.pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

[GroupyEntry4]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Books\+Cambridge Bible for Schools and Colleges\01. Genesis (1921) by Herbert Edward Ryle.pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

[GroupyEntry5]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Books\+Cambridge Bible for Schools and Colleges\02. Exodus (1918) by Samuel Rolles Driver.pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

[GroupyEntry6]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Books\@Articles\Hittite Laws.pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

[GroupyEntry7]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Books\Let My People Go!... by Steven Collins (2005)\Let My People Go!... by Steven Collins (2005).pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

------------------------------

This is the file that gets generated with the "Save Group" function:

[Group]
GroupCount=3
GroupLeft=1902
GroupTop=22
GroupRight=3802
GroupBottom=1029
GroupMax=1
Locked=0
[GroupyEntry1]
OwnerProcess=C:\Program Files\Microsoft Office\root\Office16\WINWORD.EXE
APPID=Microsoft.Office.WINWORD.EXE.15
NewTabName=
RunElevated=0
Target="D:\$\Documentation\Books\@Study Notes\Biblical\The Holy Bible - Notes.docx"
NoPatternMatching=1
MatchingClass=OpusApp
[GroupyEntry2]
OwnerProcess=C:\Program Files\Microsoft Office\root\Office16\WINWORD.EXE
APPID=Microsoft.Office.WINWORD.EXE.15
NewTabName=
RunElevated=0
SavedColour=33023
Target="D:\$\Documentation\Books\The Book of Exodus (1974) - Brevard S. Childs\The Book of Exodus (1974) - Brevard S. Childs (Converted).docx"
NoPatternMatching=1
MatchingClass=OpusApp
[GroupyEntry3]
OwnerProcess=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
APPID={6D809377-6AF0-444B-8957-A3773F02200E}\Tracker Software\PDF Editor\PDFXEdit.exe
NewTabName=
RunElevated=0
NoPatternMatching=0
CommandLine=""D:\$\Documentation\Religion\Biblical Names Pronunciations.pdf""
WorkingDirectory=C:\Program Files\Tracker Software\PDF Editor
Target=C:\Program Files\Tracker Software\PDF Editor\PDFXEdit.exe
MatchingClass=PXE:{C5309AD3-73E4-4707-B1E1-2940D8AF3B9D}

--------------------------

As you can see, quite a difference.