[SalesForce] sfdx force:source:pull Entity of type ‘CustomApplication’ named ‘Case’ cannot be found

I'll answer as I did find some kind of workaround

Those steps allow me to work DX-style with Managed Package, Namespace and Person Account

1 Create scratch org WITHOUT Namespace, using flag -n, --nonamespace

sfdx force:org:create -f config/project-scratch-def.json -a ScratchNONameSpace -s -n

2 First thing is to pull Account.Business_Account, which works as expected

$ sfdx force:source:status -r

=== Source Status
STATE       FULL NAME                 TYPE        PROJECT PATH
Remote Add  Account.Business_Account  RecordType

$ sfdx force:source:pull

=== Pulled SourceSTATE  FULL NAME                 TYPE        PROJECT PATH
Add    Account.Business_Account  RecordType  force-app/main/default/objects/Account/recordTypes/Business_Account.recordType-meta.xml

3 Create scratch org WITH Namespace

sfdx force:org:create -f config/project-scratch-def.json -a ScratchWithNameSpace -s

4 Check status, you'll see conflicts

$ sfdx force:source:status
=== Source Status
STATE                      FULL NAME                 TYPE        PROJECT PATH

Local Add (Conflict)       Account.Business_Account  RecordType  force-app/main/default/objects/Account/recordTypes/Business_Account.recordType-meta.xml
Remote Changed (Conflict)  Account.Business_Account  RecordType  force-app/main/default/objects/Account/recordTypes/Business_Account.recordType-meta.xml

5 Push your code using flag -f, --forceoverwrite

$ sfdx force:source:push -f
=== Pushed Source
STATE  FULL NAME                 TYPE        PROJECT PATH

Add    Account.Business_Account  RecordType  force-app/main/default/objects/Account/recordTypes/Business_Account.recordType-meta.xml

$ sfdx force:source:status
=== Source Status
No results found

After that you would be able to push/pull without issues.

I just went into the same problem.

I emptied the recycle bin but that didn't solve the problem.

I was able to find the references of the now removed content asserts when searching the whole project in the following file .sfdx/orgs/{scratch org username}/maxRevision.json

e.g. search ProtonTextIcon60x60 or ProtonTextIcon60x601 in your project if you're op.

Remove those references from the above mentioned file fixed it for me.