Ahhhh, okay you're using a tpk -- makes more sense.
So there is a way you can do this, but I'm sure it isn't supported. But, in case you have a test environment you can test this in, here's the workflow.
In the cache, there should be an .xml documnet (conf.xml) that has the tiling scheme. In it, you'll see several <LOD> tags which represent the various layers of detail (levels). You can delete the appropriate <LOD> from that .XML document, which will tell your tpk to not look for that level. To free up space, there should be various folders within the cache directory (1,2,3,4,5,6,7,etc.) representing the various LODs. After going to your XML and identifying the LOD that corresponds to the scale level you want to get rid of, you can then delete the corresponding folder in the _alllayers folder.
Below is an example of what all this might look like. In the below example, I am interested in deleting the scale level of 4622324.
conf.xml:
<?xml version="1.0" encoding="utf-8" ?><CacheInfo xsi:type='typens:CacheInfo' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xmlns:xs='http://www.w3.org/2001/XMLSchema' xmlns:typens='http://www.esri.com/schemas/ArcGIS/10.5'><TileCacheInfo xsi:type='typens:TileCacheInfo'><SpatialReference xsi:type='typens:ProjectedCoordinateSystem'><WKT>PROJCS["WGS_1984_Web_Mercator_Auxiliary_Sphere",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator_Auxiliary_Sphere"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",0.0],PARAMETER["Standard_Parallel_1",0.0],PARAMETER["Auxiliary_Sphere_Type",0.0],UNIT["Meter",1.0],AUTHORITY["EPSG",3857]]</WKT><XOrigin>-20037700</XOrigin><YOrigin>-30241100</YOrigin><XYScale>148923141.92838538</XYScale><ZOrigin>-100000</ZOrigin><ZScale>10000</ZScale><MOrigin>-100000</MOrigin><MScale>10000</MScale><XYTolerance>0.001</XYTolerance><ZTolerance>0.001</ZTolerance><MTolerance>0.001</MTolerance><HighPrecision>true</HighPrecision><WKID>102100</WKID><LatestWKID>3857</LatestWKID></SpatialReference><TileOrigin xsi:type='typens:PointN'><X>-20037508.342787001</X><Y>20037508.342787001</Y></TileOrigin><TileCols>256</TileCols><TileRows>256</TileRows><DPI>96</DPI><LODInfos xsi:type='typens:ArrayOfLODInfo'><LODInfo xsi:type='typens:LODInfo'><LevelID>0</LevelID><Scale>591657527.591555</Scale><Resolution>156543.03392800014</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>1</LevelID><Scale>295828763.79577702</Scale><Resolution>78271.516963999937</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>2</LevelID><Scale>147914381.89788899</Scale><Resolution>39135.758482000092</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>3</LevelID><Scale>73957190.948944002</Scale><Resolution>19567.879240999919</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>4</LevelID><Scale>36978595.474472001</Scale><Resolution>9783.9396204999593</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>5</LevelID><Scale>18489297.737236001</Scale><Resolution>4891.9698102499797</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>6</LevelID><Scale>9244648.8686180003</Scale><Resolution>2445.9849051249898</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>7</LevelID><Scale>4622324.4343090001</Scale><Resolution>1222.9924525624949</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>8</LevelID><Scale>2311162.2171550002</Scale><Resolution>611.49622628137968</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>9</LevelID><Scale>1155581.108577</Scale><Resolution>305.74811314055756</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>10</LevelID><Scale>577790.55428899999</Scale><Resolution>152.87405657041106</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>11</LevelID><Scale>288895.27714399999</Scale><Resolution>76.437028285073239</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>12</LevelID><Scale>144447.638572</Scale><Resolution>38.21851414253662</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>13</LevelID><Scale>72223.819285999998</Scale><Resolution>19.10925707126831</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>14</LevelID><Scale>36111.909642999999</Scale><Resolution>9.5546285356341549</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>15</LevelID><Scale>18055.954822</Scale><Resolution>4.7773142679493699</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>16</LevelID><Scale>9027.9774109999998</Scale><Resolution>2.3886571339746849</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>17</LevelID><Scale>4513.9887049999998</Scale><Resolution>1.1943285668550503</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>18</LevelID><Scale>2256.994353</Scale><Resolution>0.59716428355981721</Resolution></LODInfo><LODInfo xsi:type='typens:LODInfo'><LevelID>19</LevelID><Scale>1128.4971760000001</Scale><Resolution>0.29858214164761665</Resolution></LODInfo></LODInfos><PreciseDPI>96</PreciseDPI></TileCacheInfo><TileImageInfo xsi:type='typens:TileImageInfo'><CacheTileFormat>PNG</CacheTileFormat><CompressionQuality>0</CompressionQuality><Antialiasing>false</Antialiasing><BandCount>1</BandCount><LERCError>0</LERCError></TileImageInfo><CacheStorageInfo xsi:type='typens:CacheStorageInfo'><StorageFormat>esriMapCacheStorageModeCompactV2</StorageFormat><PacketSize>128</PacketSize></CacheStorageInfo></CacheInfo>
If you delete the bold text, it should remove the cache's recognition of this LOD.
Then, in the _alllayers folder, you should see a folder for each LOD. I would then delete the folder named '7' that contains the map cache bundle files.
I'd strongly advise to make backups prior to going through this workflow and doing this in a test/dev environment first. I'm traveling right now, so I can't confirm that the exploded .tpk matches this structure exactly, but when I'm back at a desktop, I can check,
