yes, there is a pretty workaround calling a vb-script at the right interupt-event. I've developed exactly what you are asking for shortly and it works like a charm.
1. Use the event-manager (Advanced -> Scripting -> Edit Events) and enter "Call( ExchangeRCHFile.vbs )" in the textbox besides "Before MODFLOW". This event fires AFTER Weap has produced its own set of MODFLOW files, but hasn't yet started MODFLOW. This is the right moment to replace the recharge file with your own.
2. Go to Advanced -> Scripting -> Edit Scripts and paste the lines below into a new document and save as ExchangeRCHFile.vbs. You will need to replace the words in brackets  with what fits to your setup!
3. The script requires:
- that you have a folder containing all recharge files under the Area Directory
- that there is one folder for each scenario underneath
- the RCH-files are named "YYYY_MM.rch"
- the formats of the RCH-files match with the formats of the files produced by WEAP
Good luck and all the best
Dim sCCRechFolder, sCCRechFile, sDestRechFile, sMFModelname, sMFFolder
Dim sScen, iScen, iYear, iMonth
sMFModelName = "[ENTER THE NAME OF YOUR MODFLOW MODEL HERE]"
sMFFolder = WEAP.ActiveArea.Directory & "MODFLOW\"
sCCRechFolder = WEAP.ActiveArea.Directory & "[ENTER THE FOLDERNAME WHERE THE RECHARGE FILES ARE]\"
'--- Generate FileNames based on current Scenario and Timestep'
sScen = WEAP.ActiveScenario.Name
iScen = Weap.ActiveScenario.ID
if len(iScen)<2 then iScen = "0" & iScen
iYear = CalcYear
iMonth = CalcTS
if len(iMonth)<2 then iMonth = "0" & iMonth
sCCRechFile = sCCRechFolder & "\" & sScen & "\" & iYear & "_" & iMonth & ".rch" 'you either need to follow this pattern in your file system, or you change the code here accordingly