The status of the bug is labeled as Won't fix and I can understand why in this context.

The right way would have been to run ALTER TABLE tbl_name DROP PARTITION; because the MySQL Documentation on ALTER TABLE Partition Operations says:

DROP PARTITION can be used to drop one or more RANGE or LIST partitions. This statement cannot be used with HASH or KEY partitions; instead, use COALESCE PARTITION (see below). Any data that was stored in the dropped partitions named in the partition_names list is discarded.

ALTER TABLE t1 DROP PARTITION p0, p1;

Once you ran ALTER TABLE tbl_name DISCARD TABLESPACE;, the data dictionary should no longer be aware of the physical presence of the orphaned .ibd files. However, since the bug does not reclaim the diskspace, perhaps the data dictionary entries for your tables is intact. Let's find out.

WARNING : You should run service mysql stop and do a physical backup of /var/lib/mysql

First do this: SHOW CREATE TABLE tbl_name\G

Then, run SELECT * FROM tbl_name WHERE (stuff from partition #x) LIMIT 10;

to test the table's usability of each partition.

Once you are confortable with the table usability, you can any of the following:

REMOVE ANY PARTITION YOU WANT

ALTER TABLE tbl_name DROP PARTITION partition-name;

If you do not trust ALTER TABLE tbl_name DROP PARTITION partition-name;, do it manually

CREATE TABLE tbl_name2 LIKE tbl_name;
ALTER TABLE tbl_name2 DROP PARTITION partition-name;
INSERT INTO tbl_name2 SELECT * FROM tbl_name WHERE (anything but stuff from partition-name)
ALTER TABLE tbl_name RENAME tbl_name9;
ALTER TABLE tbl_name2 RENAME tbl_name;
DROP TABLE tbl_name9;   

DROP ALL DATA FROM PARTITION BUT KEEP PARTITION

ALTER TABLE tbl_name TRUNCATE PARTITION partition-name;

If you do not trust ALTER TABLE tbl_name TRUNCATE PARTITION partition-name;, do it manually

CREATE TABLE tbl_name2 LIKE tbl_name;
INSERT INTO tbl_name2 SELECT * FROM tbl_name WHERE (anything but stuff from partition-name)
ALTER TABLE tbl_name RENAME tbl_name9;
ALTER TABLE tbl_name2 RENAME tbl_name;
DROP TABLE tbl_name9;   

CREATE A BLANK TABLE

CREATE TABLE tbl_name2 LIKE tbl_name;
DROP TABLE tbl_name;
ALTER TABLE tbl_name2 RENAME tbl_name;

Give it a Try !!!

UPDATE 2013-05-20 18:41 EDT

I am glad you were able to drop the partition.

I have some distressing news: It is not possible to shrink ibdata1 without dumping all the data, deleting ibdata1, restarting mysql, and reloading.

Here are my past posts on how to do that safely:

• May 21, 2012 : How large will a MySQL database be relative to the dump file?
• Apr 01, 2012 : Is innodb_file_per_table advisable?
• Mar 25, 2012 : Why does InnoDB store all databases in one file?
• Feb 04, 2011 : MySQL InnoDB - innodb_file_per_table cons?
• Oct 29, 2010 : Howto: Clean a mysql InnoDB storage engine?

What might cause the big discrepancy in disk space?

Typically this is caused by rows that have been deleted. Heaps do not reclaim space for data pages emptied by DELETE operations unless a table lock is taken at the time of the deletion. Even then, other factors like the possibility of row-overflow data, or an enabled row-versioning isolation level can prevent space being reclaimed.

Another factor that usually has a much smaller impact on space usage is that rows with variable-length columns that expand may not fit on the original heap page, in which case the row is forwarded to another page. Forwarded rows are more usually associated with scan performance issues than pure space usage, however.

Overall, tables that experience significant deletions (without the space being reused quickly by new rows) and/or variable column updates that do not fit in place are often better configured with a clustered index. Clustered tables usually deallocate empty pages very quickly.

You can use the sys.dm_db_index_physical_stats DMV to see physical details for a heap or index:

SELECT
    DDIPS.index_id,
    DDIPS.partition_number,
    DDIPS.index_type_desc,
    DDIPS.alloc_unit_type_desc,
    DDIPS.avg_fragmentation_in_percent,
    DDIPS.fragment_count,
    DDIPS.avg_fragment_size_in_pages,
    DDIPS.page_count,
    DDIPS.avg_page_space_used_in_percent,
    DDIPS.record_count,
    DDIPS.avg_record_size_in_bytes,
    DDIPS.forwarded_record_count
FROM sys.dm_db_index_physical_stats
    (
        DB_ID(),
        OBJECT_ID(N'dbo.t1', N'U'),
        0,
        NULL,
        'DETAILED'
    ) AS DDIPS;

The following (trivial) example shows a heap DELETE not releasing any empty pages:

SET NOCOUNT ON;
CREATE TABLE t1 (c1 char(8000) DEFAULT 'a'); 
GO
INSERT INTO t1 DEFAULT VALUES; 
GO 1000

-- 1000 pages allocated
SELECT
    DDIPS.index_id,
    DDIPS.partition_number,
    DDIPS.page_count
FROM sys.dm_db_index_physical_stats
    (
        DB_ID(),
        OBJECT_ID(N'dbo.t1', N'U'),
        0,
        NULL,
        'DETAILED'
    ) AS DDIPS;

-- Delete all the data from the heap
DELETE FROM t1;

-- Still 1000 pages allocated
-- Even though the table is empty
SELECT
    DDIPS.index_id,
    DDIPS.partition_number,
    DDIPS.page_count
FROM sys.dm_db_index_physical_stats
    (
        DB_ID(),
        OBJECT_ID(N'dbo.t1', N'U'),
        0,
        NULL,
        'DETAILED'
    ) AS DDIPS;
GO
DROP TABLE dbo.t1;

If you try the example again, but with a table lock (DELETE FROM t1 WITH (TABLOCK)) the deletion frees all empty pages (assuming the database does not have the READ_COMMITTED_SNAPSHOT option set to ON etc.)