Workaround for the limit of the number of missing indexes suggested by SQL Server's DMVs
You can't reset the DMVs, however you can work around this limitation and remove rows from the DMVs by creating a small filtered index on the tables mentioned in the DMVs then immediately dropping that index.

For instance:

CREATE INDEX IX_temp
ON dbo.SomeTable(SomeKey)
WHERE SomeKey IS NULL;

DROP INDEX dbo.SomeTable.IX_temp;


I've created a script to automate this process.

IF OBJECT_ID('dbo.RemoveMissingIndexSuggestions') IS NOT NULL
DROP PROCEDURE RemoveMissingIndexSuggestions;
GO
CREATE PROCEDURE dbo.RemoveMissingIndexSuggestions
(
    @Database SYSNAME = NULL --optional, if NULL, clear all suggestions
                             --if specified, only clear suggestions for that database
    , @Table SYSNAME = NULL --if not NULL, only clear suggestions for the specified table 
)
AS
BEGIN
    /*
        Max Vernon, 2016-04-08
        Inspired by work by Joe Sack and Glenn Berry at
        http://www.sqlskills.com/blogs/joe/clearing-missing-index-suggestions-for-a-single-table/

        Creates one index for each table that is mentioned in sys.dm_db_missing_index_details
        then promply drops that index.  The index is created with a WHERE clause that is likely 
        to eliminate all or almost all rows, and therefore will be created quite quickly.
    */
    SET NOCOUNT ON;
    DECLARE @ObjectName SYSNAME;
    DECLARE @DatabaseName SYSNAME;
    DECLARE @CreateStmt NVARCHAR(MAX);
    DECLARE @DropStmt NVARCHAR(MAX);
    DECLARE @stmt NVARCHAR(MAX);
    DECLARE @msg NVARCHAR(2000);
    DECLARE @vars NVARCHAR(1000);
    DECLARE @Uniquifier NVARCHAR(48);
    SET @vars = '@stmt NVARCHAR(MAX)';
    DECLARE cur CURSOR LOCAL FORWARD_ONLY STATIC
    FOR
    WITH cte AS
    (
        SELECT ObjectName = d.name + '.' + s.name + '.' + o.name
            , DatabaseName = d.name
            , CreateStmt = N'CREATE INDEX [IX_temp] 
ON ' + QUOTENAME(s.name) + N'.' + QUOTENAME(o.name) + N'(' + mid.equality_columns + N') 
WHERE ' 
              + (
                SELECT TOP(1) cols.ColName FROM (
                    SELECT TOP(1) ColName = QUOTENAME(c.name) + N' IS NULL'
                    FROM sys.columns c 
                        INNER JOIN sys.key_constraints kc ON c.object_id = kc.parent_object_id 
                    WHERE c.object_id = o.object_id 
                        AND kc.type_desc = N'PRIMARY_KEY_CONSTRAINT'
                    UNION ALL
                    SELECT TOP(1) QUOTENAME(c.name) + N' = -2147483648'
                    FROM sys.columns c
                        INNER JOIN sys.types ty ON c.system_type_id = ty.system_type_id
                    WHERE ty.name IN 
                        (
                              N'bigint'
                            , N'binary'
                            , N'hierarchyid'
                            , N'int'
                            , N'uniqueidentifier'
                            , N'varbinary'
                        )
                    ) cols
                ) 
                + ';'
                , DropStmt = N'DROP INDEX ' + QUOTENAME(s.name) + N'.' + QUOTENAME(o.name) + '.[IX_temp];'
                , rn = ROW_NUMBER() OVER (PARTITION BY mid.object_id ORDER BY mid.index_handle)
        FROM sys.dm_db_missing_index_details mid
            INNER JOIN sys.objects o ON mid.object_id = o.object_id
            INNER JOIN sys.schemas s ON o.schema_id = s.schema_id
            INNER JOIN sys.databases d ON mid.database_id = d.database_id
        WHERE o.name NOT LIKE '#%' -- ignore temp tables
            AND (d.name = @Database OR @Database IS NULL)
            AND (o.name = @Table OR @Table IS NULL)
    )
    SELECT cte.ObjectName
        , cte.DatabaseName
        , cte.CreateStmt
        , cte.DropStmt
    FROM cte
    WHERE rn = 1;
    OPEN cur;
    FETCH NEXT FROM cur INTO @ObjectName, @DatabaseName, @CreateStmt, @DropStmt;
    WHILE @@FETCH_STATUS = 0
    BEGIN
        SET @msg = 'Flushing ' + @ObjectName + ' indexes.

';
        RAISERROR (@msg, 0, 1) WITH NOWAIT;
        SET @stmt = 'EXEC ' + QUOTENAME(@DatabaseName) + '.sys.sp_executesql @stmt;'
        SET @Uniquifier = CONVERT(NVARCHAR(48), NEWID(), 0);
        SET @CreateStmt = REPLACE(@CreateStmt, '[IX_Temp]', '[IX_Temp_' + @Uniquifier + ']')
        SET @DropStmt = REPLACE(@DropStmt, '[IX_Temp]', '[IX_Temp_' + @Uniquifier + ']')
        SET @CreateStmt = 'SET ANSI_NULLS ON;
SET ANSI_PADDING ON;
SET ANSI_WARNINGS ON;
SET ARITHABORT ON;
SET CONCAT_NULL_YIELDS_NULL ON;
SET NUMERIC_ROUNDABORT OFF;
SET QUOTED_IDENTIFIER ON;
' + @CreateStmt + '

';
        SET @DropStmt = 'SET ANSI_NULLS ON;
SET ANSI_PADDING ON;
SET ANSI_WARNINGS ON;
SET ARITHABORT ON;
SET CONCAT_NULL_YIELDS_NULL ON;
SET NUMERIC_ROUNDABORT OFF;
SET QUOTED_IDENTIFIER ON;
' + @DropStmt + '

';
        RAISERROR (@CreateStmt, 0, 1) WITH NOWAIT;
        RAISERROR (@DropStmt, 0, 1) WITH NOWAIT;
        EXEC sp_executesql @stmt, @vars, @stmt = @CreateStmt;
        EXEC sp_executesql @stmt, @vars, @stmt = @DropStmt;
        FETCH NEXT FROM cur INTO @ObjectName, @DatabaseName, @CreateStmt, @DropStmt;
    END
    CLOSE cur;
    DEALLOCATE cur;
END
GO


This can be executed with the @Database parameter set to the name of a database to eliminate recommended indexes only related to that database, or without parameters to eliminate all recommended indexes.  One can optionally limit this to the suggestions for a single table by passing the name of the table into the @Table parameter.

EXEC dbo.RemoveMissingIndexSuggestions @Database = 'tempdb', @Table = 'SomeTable';


It creates at most one index per table. The index has a unique name and is constructed using a single column, giving priority to using the table's PRIMARY KEY, if it has one.  Tables will be missed by this proc if the table does not have a primary key or at least one of the following types of columns:

bigint
binary
hierarchyid
int
uniqueidentifier
varbinary


I've written a short blog post on this issue over at SQLServerScience