For me (Arch Linux, Duplicati installed from AUR) I needed to run;
sudo certmgr -del -c -v -m Trust 5BCAA1C2780F0BCB5A90770451D96F38963F012D
Why
It’s essentially the same as the solutions above, but for me deleting the certificate from the main store and running cert-sync wasn’t syncing to Mono’s certificate store properly I don’t know why.
To see if Mono still has the offending certificate you can run
>>> $ certmgr -list -certificate -m Trust | egrep --context 3 'ISRG Root X1|DST Root CA X3'
Self-signed X.509 v3 Certificate
Serial Number: 6B40F82E86393089BA27A3D680B0AF44
Issuer Name: O=Digital Signature Trust Co., CN=DST Root CA X3
Subject Name: O=Digital Signature Trust Co., CN=DST Root CA X3
Valid From: 30/09/2000 9:12:19 PM
Valid Until: 30/09/2021 2:01:15 PM
Unique Hash: 5BCAA1C2780F0BCB5A90770451D96F38963F012D
--
Self-signed X.509 v3 Certificate
Serial Number: 008B8263BBE0634459E340D2B0CF108200
Issuer Name: C=US, O=Internet Security Research Group, CN=ISRG Root X1
Subject Name: C=US, O=Internet Security Research Group, CN=ISRG Root X1
Valid From: 4/06/2015 11:04:38 AM
Valid Until: 4/06/2035 11:04:38 AM
Unique Hash: 3F0411EDE9C4477057D57E57883B1F205B20CDC0F3263129B1EE0269A2678F63
After deleting it with certmgr and running that command again I’ve only go the ISRG certificate
>>> $ certmgr -list -certificate -m Trust | egrep --context 3 'ISRG Root X1|DST Root CA X3'
Self-signed X.509 v3 Certificate
Serial Number: 008B8263BBE0634459E340D2B0CF108200
Issuer Name: C=US, O=Internet Security Research Group, CN=ISRG Root X1
Subject Name: C=US, O=Internet Security Research Group, CN=ISRG Root X1
Valid From: 4/06/2015 11:04:38 AM
Valid Until: 4/06/2035 11:04:38 AM
Unique Hash: 3F0411EDE9C4477057D57E57883B1F205B20CDC0F3263129B1EE0269A2678F63
Anyway, hopefully that helps anyone else who is similarly stuck 