I sometimes use the official Gparted Live, based on Debian sid. Though it enables contrib and non-free repositories by default, it doesn't come with any non-free software (included in the ISO). So as soon as you boot into the Live environment, disable the contrib and non-free repositories and you should have a free/libre Live environment. apt and dpkg are pre-configured, so if you need additional disk utilities, just download and install them from Debian's main repository.
Maybe you need a newer version of Gparted and try to fix the problems (if
any) with both partitions. I never use legacy versions of disk utilities
(like those in Trisquel) for such critical jobs. I recently used latest
Gparted to fix an NTFS volume which has been "sentenced to death" under
Losedows and retrieved all data. (Though I had to go to Losedows to run
"chkdsk -f" as the finishing touch to make the disk usable again.)
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