diff --git a/lib/private/repair/repairlegacystorages.php b/lib/private/repair/repairlegacystorages.php
index ab123afeca..f09ca2b5cd 100644
--- a/lib/private/repair/repairlegacystorages.php
+++ b/lib/private/repair/repairlegacystorages.php
@@ -146,76 +146,89 @@ class RepairLegacyStorages extends BasicEmitter {
 
 		$this->connection->beginTransaction();
 
-		try {
-			// note: not doing a direct UPDATE with the REPLACE function
-			// because regexp search/extract is needed and it is not guaranteed
-			// to work on all database types
-			$sql = 'SELECT `id`, `numeric_id` FROM `*PREFIX*storages`'
-				. ' WHERE `id` LIKE ?'
-				. ' ORDER BY `id`';
-			$result = $this->connection->executeQuery($sql, array($dataDirId . '%'));
-			while ($row = $result->fetch()) {
-				$currentId = $row['id'];
-				// one entry is the datadir itself
-				if ($currentId === $dataDirId) {
-					continue;
-				}
+		// note: not doing a direct UPDATE with the REPLACE function
+		// because regexp search/extract is needed and it is not guaranteed
+		// to work on all database types
+		$sql = 'SELECT `id`, `numeric_id` FROM `*PREFIX*storages`'
+			. ' WHERE `id` LIKE ?'
+			. ' ORDER BY `id`';
+		$result = $this->connection->executeQuery($sql, array($dataDirId . '%'));
 
+		while ($row = $result->fetch()) {
+			$currentId = $row['id'];
+			// one entry is the datadir itself
+			if ($currentId === $dataDirId) {
+				continue;
+			}
+
+			try {
 				if ($this->fixLegacyStorage($currentId, (int)$row['numeric_id'])) {
 					$count++;
 				}
 			}
+			catch (\OC\RepairException $e) {
+				$this->emit(
+					'\OC\Repair',
+					'warning',
+					array('Could not repair legacy storage ' . $currentId . ' automatically.')
+				);
+			}
+		}
 
-			// check for md5 ids, not in the format "prefix::"
-			$sql = 'SELECT COUNT(*) AS "c" FROM `*PREFIX*storages`'
-				. ' WHERE `id` NOT LIKE \'%::%\'';
-			$result = $this->connection->executeQuery($sql);
-			$row = $result->fetch();
-			// find at least one to make sure it's worth
-			// querying the user list
-			if ((int)$row['c'] > 0) {
-				$userManager = \OC_User::getManager();
+		// check for md5 ids, not in the format "prefix::"
+		$sql = 'SELECT COUNT(*) AS "c" FROM `*PREFIX*storages`'
+			. ' WHERE `id` NOT LIKE \'%::%\'';
+		$result = $this->connection->executeQuery($sql);
+		$row = $result->fetch();
+		// find at least one to make sure it's worth
+		// querying the user list
+		if ((int)$row['c'] > 0) {
+			$userManager = \OC_User::getManager();
 
-				// use chunks to avoid caching too many users in memory
-				$limit = 30;
-				$offset = 0;
+			// use chunks to avoid caching too many users in memory
+			$limit = 30;
+			$offset = 0;
 
-				do {
-					// query the next page of users
-					$results = $userManager->search('', $limit, $offset);
-					$storageIds = array();
-					$userIds = array();
-					foreach ($results as $uid => $userObject) {
-						$storageId = $dataDirId . $uid . '/';
-						if (strlen($storageId) <= 64) {
-							// skip short storage ids as they were handled in the previous section
-							continue;
-						}
-						$storageIds[$uid] = $storageId;
+			do {
+				// query the next page of users
+				$results = $userManager->search('', $limit, $offset);
+				$storageIds = array();
+				$userIds = array();
+				foreach ($results as $uid => $userObject) {
+					$storageId = $dataDirId . $uid . '/';
+					if (strlen($storageId) <= 64) {
+						// skip short storage ids as they were handled in the previous section
+						continue;
 					}
+					$storageIds[$uid] = $storageId;
+				}
 
-					if (count($storageIds) > 0) {
-						// update the storages of these users
-						foreach ($storageIds as $uid => $storageId) {
-							$numericId = \OC\Files\Cache\Storage::getNumericStorageId($storageId);
+				if (count($storageIds) > 0) {
+					// update the storages of these users
+					foreach ($storageIds as $uid => $storageId) {
+						$numericId = \OC\Files\Cache\Storage::getNumericStorageId($storageId);
+						try {
 							if (!is_null($numericId) && $this->fixLegacyStorage($storageId, (int)$numericId)) {
 								$count++;
 							}
 						}
+						catch (\OC\RepairException $e) {
+							$this->emit(
+								'\OC\Repair',
+								'warning',
+								array('Could not repair legacy storage ' . $storageId . ' automatically.')
+							);
+						}
 					}
-					$offset += $limit;
-				} while (count($results) >= $limit);
-			}
-
-			$this->emit('\OC\Repair', 'info', array('Updated ' . $count . ' legacy home storage ids'));
-
-			$this->connection->commit();
-		}
-		catch (\OC\RepairException $e) {
-			$this->connection->rollback();
-			throw $e;
+				}
+				$offset += $limit;
+			} while (count($results) >= $limit);
 		}
 
+		$this->emit('\OC\Repair', 'info', array('Updated ' . $count . ' legacy home storage ids'));
+
+		$this->connection->commit();
+
 		$this->config->setAppValue('core', 'repairlegacystoragesdone', 'yes');
 	}
 }
diff --git a/tests/lib/repair/repairlegacystorage.php b/tests/lib/repair/repairlegacystorage.php
index f08393300e..24f2dbe13c 100644
--- a/tests/lib/repair/repairlegacystorage.php
+++ b/tests/lib/repair/repairlegacystorage.php
@@ -24,6 +24,8 @@ class TestRepairLegacyStorages extends \Test\TestCase {
 	private $legacyStorageId;
 	private $newStorageId;
 
+	private $warnings;
+
 	protected function setUp() {
 		parent::setUp();
 
@@ -32,6 +34,12 @@ class TestRepairLegacyStorages extends \Test\TestCase {
 		$this->oldDataDir = $this->config->getSystemValue('datadirectory', \OC::$SERVERROOT . '/data/');
 
 		$this->repair = new \OC\Repair\RepairLegacyStorages($this->config, $this->connection);
+
+		$this->warnings = [];
+
+		$this->repair->listen('\OC\Repair', 'warning', function ($description){
+			$this->warnings[] = $description;
+		});
 	}
 
 	protected function tearDown() {
@@ -181,22 +189,17 @@ class TestRepairLegacyStorages extends \Test\TestCase {
 		$this->createData($this->legacyStorageId);
 		$this->createData($this->newStorageId);
 
-		try {
-			$thrown = false;
-			$this->repair->run();
-		}
-		catch (\OC\RepairException $e) {
-			$thrown = true;
-		}
+		$this->repair->run();
 
-		$this->assertTrue($thrown);
+		$this->assertEquals(1, count($this->warnings));
+		$this->assertEquals('Could not repair legacy storage ', substr(current($this->warnings), 0, 32));
 
 		// storages left alone
 		$this->assertEquals($legacyStorageNumId, $this->getStorageId($this->legacyStorageId));
 		$this->assertEquals($newStorageNumId, $this->getStorageId($this->newStorageId));
 
-		// did not set the done flag
-		$this->assertNotEquals('yes', $this->config->getAppValue('core', 'repairlegacystoragesdone'));
+		// set the done flag
+		$this->assertEquals('yes', $this->config->getAppValue('core', 'repairlegacystoragesdone'));
 	}
 
 	/**