Just a guess, and probably a fix, I face a similar problem on Opportunity,
Shortcut explanation is doctype json file have attribute “modified” date inside. Doctype into TabDocType table have also column modified date.
If they are the same during the patch update, frappe.reload_doc test it and do not perform ALTER TABLE column modify…
So two solutions
1 - Sql before launch bench upgrade --patch or switch to branch
UPDATE tabDocType SET modified=‘2020-09-08 11:10:35.318872’ WHERE name=‘Stock Ledger Entry’
2- change de docyte json file modifed attribute and commit before launch bench upgrade --patch
I’ve just submit a PR for Opportunity migration bug.
Second guess… Some developpement are back ported from v13 or develop into v12 with the same modified date into json doctype file, and this is a real bad practice regarding how upgrade process works.
If some column name change, this json doctype “modified” must be different between version…