diff --git a/docs/changelog.md b/docs/changelog.md
index 39162018..fe00b7bc 100644
--- a/docs/changelog.md
+++ b/docs/changelog.md
@@ -11,6 +11,7 @@
 
 - [promql/vector_matching](checks/promql/vector_matching.md) will now report more details, including which Prometheus server reports problems and which part of the query is the issue.
 - GitHub report code was refactored, it should behave as before.
+- When running `pint ci` pint will now run all checks on unmodified rules when a `file/disable` comment was removed.
 
 ### Fixed
 
diff --git a/internal/discovery/git_branch.go b/internal/discovery/git_branch.go
index ba9f45ef..91b40ae8 100644
--- a/internal/discovery/git_branch.go
+++ b/internal/discovery/git_branch.go
@@ -4,6 +4,7 @@ import (
 	"bytes"
 	"fmt"
 	"log/slog"
+	"sort"
 	"strings"
 
 	"golang.org/x/exp/slices"
@@ -275,7 +276,7 @@ func matchEntries(before, after []Entry) (ml []matchedEntry) {
 			if !matched && a.Rule.Name() != "" && a.Rule.IsIdentical(b.Rule) {
 				m.before = b
 				m.hasBefore = true
-				m.isIdentical = true
+				m.isIdentical = isEntryIdentical(b, a)
 				m.wasMoved = a.Path.Name != b.Path.Name
 				matched = true
 				slog.Debug(
@@ -317,6 +318,16 @@ func matchEntries(before, after []Entry) (ml []matchedEntry) {
 	return ml
 }
 
+func isEntryIdentical(b, a Entry) bool {
+	if !slices.Equal(sort.StringSlice(b.DisabledChecks), sort.StringSlice(a.DisabledChecks)) {
+		slog.Debug("List of disabled checks was modified",
+			slog.Any("before", sort.StringSlice(b.DisabledChecks)),
+			slog.Any("after", sort.StringSlice(a.DisabledChecks)))
+		return false
+	}
+	return true
+}
+
 func findRulesByName(entries []Entry, name string, typ parser.RuleType) (nomatch, match []Entry) {
 	for _, entry := range entries {
 		if entry.PathError == nil && entry.Rule.Type() == typ && entry.Rule.Name() == name {
diff --git a/internal/discovery/git_branch_test.go b/internal/discovery/git_branch_test.go
index cbc6a09f..2f2a8990 100644
--- a/internal/discovery/git_branch_test.go
+++ b/internal/discovery/git_branch_test.go
@@ -1071,6 +1071,62 @@ groups:
 				},
 			},
 		},
+		{
+			title: "file/disable comment removed",
+			setup: func(t *testing.T) {
+				commitFile(t, "rules.yml", `
+# pint file/disable promql/series
+
+- alert: rule1
+  expr: sum(foo) by(job)
+- alert: rule2
+  expr: sum(foo) by(job)
+- alert: rule3
+  expr: sum(foo) by(job)
+`, "v1")
+
+				_, err := git.RunGit("checkout", "-b", "v2")
+				require.NoError(t, err, "git checkout v2")
+
+				commitFile(t, "rules.yml", `
+
+
+- alert: rule1
+  expr: sum(foo) by(job)
+- alert: rule2
+  expr: sum(foo) by(job)
+- alert: rule3
+  expr: sum(foo) by(job)
+`, "v2")
+			},
+			finder: discovery.NewGitBranchFinder(git.RunGit, git.NewPathFilter(includeAll, nil, includeAll), "main", 4),
+			entries: []discovery.Entry{
+				{
+					State: discovery.Modified,
+					Path: discovery.Path{
+						Name:          "rules.yml",
+						SymlinkTarget: "rules.yml",
+					},
+					Rule: mustParse(3, "- alert: rule1\n  expr: sum(foo) by(job)\n"),
+				},
+				{
+					State: discovery.Modified,
+					Path: discovery.Path{
+						Name:          "rules.yml",
+						SymlinkTarget: "rules.yml",
+					},
+					Rule: mustParse(5, "- alert: rule2\n  expr: sum(foo) by(job)\n"),
+				},
+				{
+					State: discovery.Modified,
+					Path: discovery.Path{
+						Name:          "rules.yml",
+						SymlinkTarget: "rules.yml",
+					},
+					Rule: mustParse(7, "- alert: rule3\n  expr: sum(foo) by(job)\n"),
+				},
+			},
+		},
 	}
 
 	for _, tc := range testCases {