Mac – Can’t uninstall some MacPort packages: “Error: port deactivate failed: this entry does not own the given file”

I'm trying to reinstall MacPorts a long time after a system upgrade. Following the instructions (https://trac.macports.org/wiki/Migration) I was deleting the existing packages with

sudo port -f uninstall installed

but some packages failed to uninstall, like this one:

$ sudo port -fp uninstall htop
--->  Deactivating htop @2.0.2_0
Error: Failed to deactivate htop: this entry does not own the given file
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_htop-2.0.2_0_8c865ba69295476c0e7a128dde4e99667e096af21713a15e5017549bae60ccfb-949/htop/main.log for details.
Warning: Failed to execute portfile from registry for htop @2.0.2_0
--->  Deactivating htop @2.0.2_0
Error: Failed to uninstall htop: this entry does not own the given file
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_htop-2.0.2_0_8c865ba69295476c0e7a128dde4e99667e096af21713a15e5017549bae60ccfb-949/htop/main.log for details.
Warning: Failed to execute portfile from registry for htop @2.0.2_0
--->  Deactivating htop @2.0.2_0
Error: Failed to deactivate htop: this entry does not own the given file
Error: See /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_htop-2.0.2_0_8c865ba69295476c0e7a128dde4e99667e096af21713a15e5017549bae60ccfb-949/htop/main.log for details.
Warning: Failed to execute portfile from registry for htop @2.0.2_0
--->  Deactivating htop @2.0.2_0
Error: port uninstall failed: this entry does not own the given file

The mentioned file is not that helpful either:

:msg:deactivate --->  Deactivating htop @2.0.2_0
:error:deactivate Failed to deactivate htop: this entry does not own the given file
:debug:deactivate Error code: registry::invalid
:debug:deactivate Backtrace: this entry does not own the given file
:debug:deactivate     while executing
:debug:deactivate "$port deactivate $imagefiles"
:debug:deactivate     invoked from within
:debug:deactivate "registry::write {
:debug:deactivate                 $port deactivate $imagefiles
:debug:deactivate                 foreach file $files {
:debug:deactivate                     _deactivate_file $file
:debug:deactivate       ..."
:debug:deactivate     invoked from within
:debug:deactivate "try {
:debug:deactivate         # Block the TERM and INT signals to avoid being interrupted. Note that
:debug:deactivate         # they might already be block at this point because
:debug:deactivate      ..."
:debug:deactivate     (procedure "_deactivate_contents" line 39)
:debug:deactivate     invoked from within
:debug:deactivate "_deactivate_contents $requested [$requested files] $force"
:debug:deactivate     (procedure "portimage::deactivate" line 57)
:debug:deactivate     invoked from within
:debug:deactivate "registry_deactivate $subport $version $revision $portvariants [array get user_options]"
:debug:deactivate     (procedure "portdeactivate::deactivate_main" line 10)
:debug:deactivate     invoked from within
:debug:deactivate "$procedure $targetname"

I tried to clean and deactivate the packages, but still no luck, deactivation also fails the same way. Should I try to mess with the sqlite database and delete the entries manually? It seems only to contain the bad packages:

$ sudo sqlite3 registry.db 
SQLite version 3.19.3 2017-06-27 16:48:08
Enter ".help" for usage hints.
sqlite> .tables
dependencies  files         metadata      portgroups    ports       
sqlite> select * from ports;
2753|p11-kit|3e3faa778ecfd28430bbe315280dc341c966441683d37d94a4024d7748d0b7cb-1683|/opt/local/var/macports/software/p11-kit/p11-kit-0.23.2_1.darwin_16.x86_64.tbz2|0|0.23.2|1|||installed|1481028113|image|x86_64|0|darwin|16|none|0
2760|xbitmaps|d0453d7e97c5ef303ba12583cf774f04d96bfdda76e47bf1c18a6944c273080b-805|/opt/local/var/macports/software/xbitmaps/xbitmaps-1.1.1_0.darwin_16.noarch.tbz2|0|1.1.1|0|||installed|1481028131|image|noarch|0|darwin|16|none|0
2782|xorg-util-macros|262e72a94b787a522dcb652a4c3643dc331e516f2aa715062b1c3ca00b1ba912-780|/opt/local/var/macports/software/xorg-util-macros/xorg-util-macros-1.19.0_0.darwin_16.noarch.tbz2|0|1.19.0|0|||installed|1481028739|image|noarch|0|darwin|16|none|0
2791|poppler-data|8bfccdaf843aa84f3983dab2b792a00e2ddb60b9be3e5194532f69df974fdb0e-1013|/opt/local/var/macports/software/poppler-data/poppler-data-0.4.7_0.darwin_16.noarch.tbz2|0|0.4.7|0|||installed|1481030116|image|noarch|0|darwin|16|none|0
2805|p5.24-algorithm-diff|20d724c44989c8a1b452a6ff3458ac2b307b7582d8777f39bcb0e47d6a0e9ded-1293|/opt/local/var/macports/software/p5.24-algorithm-diff/p5.24-algorithm-diff-1.190.300_0.darwin_16.noarch.tbz2|0|1.190.300|0|||installed|1481030356|image|noarch|0|darwin|16|none|0
2919|htop|8c865ba69295476c0e7a128dde4e99667e096af21713a15e5017549bae60ccfb-949|/opt/local/var/macports/software/htop/htop-2.0.2_0.darwin_16.x86_64.tbz2|1|2.0.2|0|||installed|1482232073|image|x86_64|1|darwin|16|none|0
2933|pkgconfig|41f1bec966161e029163156824d434f599d70e58638639db369f380b19057459-1991|/opt/local/var/macports/software/pkgconfig/pkgconfig-0.29.2_0.darwin_16.x86_64.tbz2|0|0.29.2|0|||installed|1490785772|image|x86_64|0|darwin|16|none|0
3035|ossp-uuid|679100994c7d2fc1932795e073581709ae3faacb61aceb88dfd99ff6422adf06-3998|/opt/local/var/macports/software/ossp-uuid/ossp-uuid-1.6.2_9+perl5_24.darwin_16.x86_64.tbz2|0|1.6.2|9|+perl5_24||installed|1494806679|image|x86_64|0|darwin|16|none|0
3047|p11-kit|f0e2db7b00d411016b8cd109d061d4436941234fdd0cf0f84d8d792804202eb5-1489|/opt/local/var/macports/software/p11-kit/p11-kit-0.23.18.1_0.darwin_17.x86_64.tbz2|0|0.23.18.1|0|||imaged|1577965184|image|x86_64|0|darwin|17|none|0
sqlite>