I suspect this is a bug in the underlying Duplicity and not in Deja-Dup itself.
I seem to be affected by the same issue you describe with deleted files not being available for restore after an incremental backup.
I followed the same basic steps you mentioned above, but by calling duplicity directly in the terminal.

1. Perform a full backup of a test dir with two test files to a new bkup_dir. (file:///mnt/bkup_dir/)
2. Verify the backup has the two test files with the duplicity list-current-files command
3. Delete one of the two test files.
4. Restart the duplicity Backup (perform an incremental Backup)
5. Now the duplicity list-current-files command only shows the un-deleted file. The file deleted before the incremental backup is not available for restore.
(The terminal output below shows this process on my Ubuntu 16.04 LTS laptop)

Extra. If I delete the incremental backup files that duplicity created from step 4, leaving only the original full backup files, then duplicity will list both test files available for restore.

testuser@systemname:~$ mkdir TestOrigin
testuser@systemname:~$ cd TestOrigin
testuser@systemname:~/TestOrigin$ duplicity --version
duplicity 0.7.06
testuser@systemname:~/TestOrigin$ uname -a
Linux systemname 4.4.0-72-generic #93-Ubuntu SMP Fri Mar 31 14:07:23 UTC 2017 i686 i686 i686 GNU/Linux
testuser@systemname:~/TestOrigin$ touch test1.txt test2.txt
testuser@systemname:~/TestOrigin$ ls -al
total 8
drwxrwxr-x  2 testuser testuser 4096 Apr 15 20:23 .
drwxr-xr-x 17 testuser testuser 4096 Apr 15 20:38 ..
-rw-rw-r--  1 testuser testuser    0 Apr 15 20:23 test1.txt
-rw-rw-r--  1 testuser testuser    0 Apr 15 20:23 test2.txt
testuser@systemname:~/TestOrigin$ duplicity --no-encryption ~/TestOrigin/ file:///mnt/bkup_dir/
Local and Remote metadata are synchronized, no sync needed.
Last full backup date: none
No signatures found, switching to full backup.
--------------[ Backup Statistics ]--------------
StartTime 1492304293.46 (Sat Apr 15 20:58:13 2017)
EndTime 1492304293.47 (Sat Apr 15 20:58:13 2017)
ElapsedTime 0.01 (0.01 seconds)
SourceFiles 3
SourceFileSize 4096 (4.00 KB)
NewFiles 3
NewFileSize 4096 (4.00 KB)
DeletedFiles 0
ChangedFiles 0
ChangedFileSize 0 (0 bytes)
ChangedDeltaSize 0 (0 bytes)
DeltaEntries 3
RawDeltaSize 0 (0 bytes)
TotalDestinationSizeChange 145 (145 bytes)
Errors 0
-------------------------------------------------

testuser@systemname:~/TestOrigin$ duplicity list-current-files file:///mnt/bkup_dir/
Local and Remote metadata are synchronized, no sync needed.
Last full backup date: Sat Apr 15 20:58:13 2017
Sat Apr 15 20:23:51 2017 .
Sat Apr 15 20:23:43 2017 test1.txt
Sat Apr 15 20:23:43 2017 test2.txt
testuser@systemname:~/TestOrigin$ rm test2.txt
testuser@systemname:~/TestOrigin$ ls -al
total 8
drwxrwxr-x  2 testuser testuser 4096 Apr 15 21:02 .
drwxr-xr-x 17 testuser testuser 4096 Apr 15 21:01 ..
-rw-rw-r--  1 testuser testuser    0 Apr 15 20:23 test1.txt
testuser@systemname:~/TestOrigin$ duplicity --no-encryption ~/TestOrigin/ file:///mnt/bkup_dir/
Local and Remote metadata are synchronized, no sync needed.
Last full backup date: Sat Apr 15 20:58:13 2017
--------------[ Backup Statistics ]--------------
StartTime 1492304670.55 (Sat Apr 15 21:04:30 2017)
EndTime 1492304670.56 (Sat Apr 15 21:04:30 2017)
ElapsedTime 0.01 (0.01 seconds)
SourceFiles 2
SourceFileSize 4096 (4.00 KB)
NewFiles 1
NewFileSize 4096 (4.00 KB)
DeletedFiles 1
ChangedFiles 0
ChangedFileSize 0 (0 bytes)
ChangedDeltaSize 0 (0 bytes)
DeltaEntries 2
RawDeltaSize 0 (0 bytes)
TotalDestinationSizeChange 141 (141 bytes)
Errors 0
-------------------------------------------------
testuser@systemname:~/TestOrigin$ duplicity list-current-files file:///mnt/bkup_dir/
Local and Remote metadata are synchronized, no sync needed.
Last full backup date: Sat Apr 15 20:58:13 2017
Sat Apr 15 21:02:17 2017 .
Sat Apr 15 20:23:43 2017 test1.txt