diff --git a/CHANGELOG.next.asciidoc b/CHANGELOG.next.asciidoc
index 4899fde2f69..71851469564 100644
--- a/CHANGELOG.next.asciidoc
+++ b/CHANGELOG.next.asciidoc
@@ -91,6 +91,7 @@ https://github.com/elastic/beats/compare/v7.0.0-alpha2...master[Check the HEAD d
 - Fix redis key setting not allowing upper case characters. {pull}18854[18854] {issue}18640[18640]
 - Fix potential race condition in fingerprint processor. {pull}18738[18738]
 - Fix seccomp policy for calls to `chmod` and `chown`. {pull}20054[20054]
+- Fix issue in autodiscover that kept inputs stopped after config updates. {pull}20305[20305]
 
 *Auditbeat*
 
diff --git a/filebeat/input/errors.go b/filebeat/input/errors.go
new file mode 100644
index 00000000000..098156abf91
--- /dev/null
+++ b/filebeat/input/errors.go
@@ -0,0 +1,32 @@
+// Licensed to Elasticsearch B.V. under one or more contributor
+// license agreements. See the NOTICE file distributed with
+// this work for additional information regarding copyright
+// ownership. Elasticsearch B.V. licenses this file to you under
+// the Apache License, Version 2.0 (the "License"); you may
+// not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing,
+// software distributed under the License is distributed on an
+// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+// KIND, either express or implied.  See the License for the
+// specific language governing permissions and limitations
+// under the License.
+
+package input
+
+import (
+	"fmt"
+)
+
+// ErrInputNotFinished struct for reporting errors related to not finished inputs
+type ErrInputNotFinished struct {
+	State string
+}
+
+// Error method of ErrInputNotFinished
+func (e *ErrInputNotFinished) Error() string {
+	return fmt.Sprintf("Can only start an input when all related states are finished: %+v", e.State)
+}
diff --git a/filebeat/input/file/state.go b/filebeat/input/file/state.go
index dde3c6c5421..9ce053cdf27 100644
--- a/filebeat/input/file/state.go
+++ b/filebeat/input/file/state.go
@@ -18,6 +18,7 @@
 package file
 
 import (
+	"fmt"
 	"os"
 	"strconv"
 	"strings"
@@ -97,3 +98,19 @@ func (s *State) IsEmpty() bool {
 		len(s.Meta) == 0 &&
 		s.Timestamp.IsZero()
 }
+
+// String returns string representation of the struct
+func (s *State) String() string {
+	return fmt.Sprintf(
+		"{Id: %v, Finished: %v, Fileinfo: %v, Source: %v, Offset: %v, Timestamp: %v, TTL: %v, Type: %v, Meta: %v, FileStateOS: %v}",
+		s.Id,
+		s.Finished,
+		s.Fileinfo,
+		s.Source,
+		s.Offset,
+		s.Timestamp,
+		s.TTL,
+		s.Type,
+		s.Meta,
+		s.FileStateOS)
+}
diff --git a/filebeat/input/log/input.go b/filebeat/input/log/input.go
index b3cf4049551..67bf582eacb 100644
--- a/filebeat/input/log/input.go
+++ b/filebeat/input/log/input.go
@@ -170,7 +170,7 @@ func (p *Input) loadStates(states []file.State) error {
 
 			// In case a input is tried to be started with an unfinished state matching the glob pattern
 			if !state.Finished {
-				return fmt.Errorf("Can only start an input when all related states are finished: %+v", state)
+				return &input.ErrInputNotFinished{State: state.String()}
 			}
 
 			// Update input states and send new states to registry
diff --git a/filebeat/input/runnerfactory.go b/filebeat/input/runnerfactory.go
index a47e848bc6d..9f802c3a934 100644
--- a/filebeat/input/runnerfactory.go
+++ b/filebeat/input/runnerfactory.go
@@ -60,5 +60,9 @@ func (r *RunnerFactory) Create(
 
 func (r *RunnerFactory) CheckConfig(cfg *common.Config) error {
 	_, err := r.Create(pipeline.NewNilPipeline(), cfg, nil)
+	if _, ok := err.(*ErrInputNotFinished); ok {
+		// error is related to state, and hence config can be considered valid
+		return nil
+	}
 	return err
 }