好像 MSCK REPAIR TABLE 不会删除指向丢失目录的分区，但会列出这些分区（请参阅 Partitions not in metastore: )，因此只需编写一点脚本/手动操作，就可以根据给定的列表删除它们。

hive> create table mytable (i int) partitioned by (p int);
OK
Time taken: 0.539 seconds

hive> !mkdir mytable/p=1;
hive> !mkdir mytable/p=2;
hive> !mkdir mytable/p=3;

hive> msck repair table mytable;
OK
Partitions not in metastore:    mytable:p=1 mytable:p=2 mytable:p=3
Repair: Added partition to metastore mytable:p=1
Repair: Added partition to metastore mytable:p=2
Repair: Added partition to metastore mytable:p=3
Time taken: 0.918 seconds, Fetched: 4 row(s)

hive> show partitions mytable;
OK
p=1
p=2
p=3
Time taken: 0.331 seconds, Fetched: 3 row(s)

hive> !rmdir mytable/p=1;
hive> !rmdir mytable/p=2;
hive> !rmdir mytable/p=3;

hive> msck repair table mytable;
OK
Partitions missing from filesystem: mytable:p=1 mytable:p=2 mytable:p=3
Time taken: 0.425 seconds, Fetched: 1 row(s)

hive> show partitions mytable;
OK
p=1
p=2
p=3
Time taken: 0.56 seconds, Fetched: 3 row(s)

MSCK REPAIR TABLE <tablename> 我也面临同样的问题，我找到了解决办法，
我们知道'msck repair'命令基于目录添加分区，所以首先删除所有分区

hive>ALTER TABLE mytable drop if exists partitions(p<>'');

上面的命令删除所有分区，
然后使用 msck repair 命令，然后它将从表位置的目录创建分区。

hive>msck repair table mytable