I used Disk Utility to remove /dev/sda5 partition, and all partitions with
higher numbers have been renamed starting from 5 instead of 6. All these
partitions belong to Debian install. Consequently GRUB set the wrong root and
/etc/fstab contained wrong partition numbers.
Other tools like gparted and fdisk didn't allow me to remove that partition.

this is the new partition table, from fdisk:

   Device Boot      Start         End      Blocks   Id  System
/dev/sda1   *           1        3060    24579040+  a5  FreeBSD
Partition 1 does not end on cylinder boundary.
/dev/sda3            3061       19457   131708902+   f  W95 Ext'd (LBA)
Partition 3 does not end on cylinder boundary.
/dev/sda5   *        3061        5610    20482812   83  Linux
/dev/sda6            5611        6247     5116671   83  Linux
/dev/sda7            6248        6566     2562336   82  Linux swap / Solaris
/dev/sda8            6567       15633    72830646   83  Linux

i don't have the older, but all partitions >= sda5 were numbered from 6 and
there was sda5 after swap.
Let me know how I can provide more info.

Hello.

after documenting more on logical partitions I understood that it's not
a bug, but the expected result of removing a logical partition different
than the latest. I'm sorry for noise.
However, Disk Utility assumed I was knowing what I was doing; maybe an
info message linking to docs can be useful before confirming the action,
as it's a graphical tool and is easily accessible.

Anne